AMBER Archive (2009)

Subject: RE: [AMBER] question of ibelly used in pmemd

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 20 2009 - 12:32:08 CDT

Hi Xiaoqin,

I thought I would add my 2c to this discussion. Firstly I just want to give
a caution with regards to the use of ibelly. That is that you really not use
it!!! It simply zeros the forces and is in no way correct or physical.
Especially if you start doing things like NPT simulations with it. In this
case your virial will be wrong, you pressure will be wrong and thus your
density will be wrong. If you must restrain things then you should probably
use harmonic restraints.

Note, things like seeing a 200K temperature drop on the first step makes
sense with using belly for such a huge portion of your syste, If you are
starting from a restart file where things were not frozen and then you
suddenly freeze a chunk of it you have just magically destroyed a ton of
kinetic energy...

With regards to the problems you are seeing this could be because of all
sorts of issues including trying to do NPT with ibelly. One thing to try is
make sure you set nscm=0 when doing Belly runs, Sander may be doing this
while pmemd is not. Second make sure you do not try to use langevin dynamics
(ntt=3) with ibelly since it will likely not work.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of xiaoqin huang
> Sent: Monday, July 20, 2009 10:21 AM
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] question of ibelly used in pmemd
>
>
> 1)thanks Kristina, for your sharing of these information.
> since ibelly=1, works in your NVE MD by pmemd, and works in my NTP MD
> by sander, but why not work in my NTP MD by pmemd?
>
> 2)in your nmropt=1 and ibelly=1 input file, try to put another "&end"
> or "/" just after your line of "DISANG=Dummy.rst", then possibly will
> read in all your input.
>
> 3)I am gzipping my files, and I will send to you: Bob Duke.
>
> all the best
>
> xiaoqin
>
> 07/20/2009
>
>
>
>
> > From: Kristina.Furse.1_at_nd.edu
> > To: amber_at_ambermd.org
> > Date: Mon, 20 Jul 2009 12:56:26 -0400
> > Subject: RE: [AMBER] question of ibelly used in pmemd
> >
> >
> > > what I doubt now is not the nmropt=1 in pmemd, I doubt ibelly=1 can
> be used in pmemd or not.
> >
> > This is not the case--I am running pmemd w/belly as we speak, with
> the following input:
> >
> > DNA/counarin: 100ps NVE MD belly
> > &cntrl
> > imin = 0, irest = 1, ntx = 7,
> > ntb = 1,
> > ntt = 0,
> > cut = 10,
> > ntc = 2, ntf = 2,
> > tol = 0.0000001,
> > ntr = 0,
> > ibelly = 1,
> > iwrap = 1,
> > nstlim = 50000, dt = 0.002,
> > ntpr = 100, ntwx = 50, ntwr = 1000
> > /
> > Movable belly for water and ions
> > RES 25 9985
> > END
> > END
> >
> > Works just fine. I did run into a problem when I tried to run
> ibelly=1 and nmropt=1, though. Unlike Xiaoqin, it was a problem reading
> in the input, not with the simulation itself. I wasn't using any actual
> nmr distance restraints, I just wanted a temperature ramp so I used the
> nmr weights with a dummy (empty) DISANG file, as follows:
> >
> > DNA: 50ps NVT MD with temperature ramp
> > &cntrl
> > imin = 0, irest = 0, ntx = 1,
> > ntb = 1,
> > ntt = 1, tautp = 0.2,
> > tempi = 0.0, temp0 = 300.0, nmropt = 1,
> > cut = 10,
> > ntc = 2, ntf = 2,
> > ibelly = 1,
> > iwrap = 1,
> > nstlim = 25000, dt = 0.002,
> > ntpr = 100, ntwx = 100, ntwr = 1000
> > /
> > &wt
> > type='TEMP0', istep1=0, istep2=10000,
> > value1=0.0, value2=300.0,
> > /
> > &wt
> > type='TEMP0', istep1=10000, istep2=25000,
> > value1=300.0, value2=300.0,
> > /
> > &wt
> > type='END',
> > /
> > DISANG=Dummy.rst
> > Movable belly for water and ions
> > RES 25 9985
> > END
> > END
> >
> > This input file works fine in sander, but pmemd did not parse it
> correctly. Unfortunately, I deleted the output file a couple of days
> ago, and can't run another test right now b/c of issues with our
> cluster, but I believe it was trying to interpret the
> "DISANG=Dummy.rst" line as belly group input, and never read in the
> weight changes. I can re-run the test as soon as our cluster problems
> are resolved. Bob--I'm not sure why Xiaoqin's input was read in and
> mine wasn't, but I can look into that too.
> >
> > Kristina
> >
> >
> >
> > > From: rduke_at_email.unc.edu
> > > To: amber_at_ambermd.org
> > > Subject: Re: [AMBER] question of ibelly used in pmemd
> > > Date: Mon, 20 Jul 2009 11:53:50 -0400
> > >
> > > Well, okay, but I then can't verify/identify/fix the problem if you
> don't
> > > send me the system. Also, I find a 140K temperature drop in one
> step to be
> > > a little strange... As I say, it is possible that all aspects of
> the nmr
> > > restraints have not been checked out in the pmemd code, simply
> because I
> > > don't have test cases (this is a complaint I have had about our
> test suites
> > > for some time; since I don't use nmr restraints myself, I am not
> going to
> > > develop test cases). I would appreciate it if other folks who
> actually work
> > > with nmr restraints look at this system and see if they notice
> anything a
> > > bit unusual about it, or if some rarely tested code is being run
> here. I
> > > would also note that the minute you use nmropt = 1, pmemd speedup
> is reduced
> > > because I don't do the standard pmemd system decomposition, but
> instead
> > > behave more like sander. This was done precisely because I did not
> have
> > > test cases... I have modified the (ancient) nmr code to the
> minimum extent
> > > possible.
> > > Regards - Bob Duke
> > > ----- Original Message -----
> > > From: "xiaoqin huang" <xqhuang1018_at_msn.com>
> > > To: <amber_at_ambermd.org>
> > > Sent: Monday, July 20, 2009 11:20 AM
> > > Subject: RE: [AMBER] question of ibelly used in pmemd
> > >
> > >
> > >
> > > I first used sander for the same system, it has run well. Actually
> I used
> > > sander routinely with the same input file, i.e NMR restratint,
> ibelly
> > > groups.
> > >
> > > I tried to switch from sander to pmemd is that it is said pmemd is
> better
> > > paralleled and faster than sander, so I hoped that I would get the
> same
> > > output within much less time. but now I wasted so much time.
> > >
> > > so I tested pmemd, and at the same time keep running sander for the
> same
> > > system, and I already got what I want from running sander.
> > >
> > > p.s. the T=444.30 at the fist step (NSTEP=0) of output by pmemd is
> the same
> > > as that of the output by sander as I set ntx=1, irest=0,ig=2858,
> then sander
> > > outputs:
> > > NSTEP = 2 TIME(PS) = 200.002 TEMP(K) = 298.08
> > >
> > > please see the attached file for the output of pmemd.
> > >
> > >
> > >
> > >
> > > > From: rduke_at_email.unc.edu
> > > > To: amber_at_ambermd.org
> > > > Subject: Re: [AMBER] question of ibelly used in pmemd
> > > > Date: Mon, 20 Jul 2009 10:42:15 -0400
> > > >
> > > > The IMPORTANT question is: Does sander work, or not, in the same
> > > > situation?
> > > > The distinction we are looking for is whether or not there is a
> possible
> > > > bug
> > > > in pmemd. Given your initial conditions, with the temperature at
> 444 or
> > > > whatever it is, and a rapid rise in one step, there is a very
> high
> > > > probability that there is a problem not with pmemd, but with your
> model
> > > > system. The only reason I am marginally unsure is there is some
> > > > possibility
> > > > in some untested aspect of the nmr code in pmemd. If that is the
> case,
> > > > sander would work, and pmemd wouldn't. So if you want help,
> either do the
> > > > test I am asking you to do, or send me the system...
> > > > Regards - Bob Duke
> > > > ----- Original Message -----
> > > > From: "xiaoqin huang" <xqhuang1018_at_msn.com>
> > > > To: <amber_at_ambermd.org>
> > > > Sent: Monday, July 20, 2009 10:21 AM
> > > > Subject: RE: [AMBER] question of ibelly used in pmemd
> > > >
> > > >
> > > >
> > > > thanks for your reply for so much detail!
> > > >
> > > > actually, the pmemd (amber 9), DOES NOT work (MD simulations)
> with
> > > > ibelly=1.
> > > >
> > > > When only ibelly=1, without any other restraints (no NMR
> restraints), it
> > > > read in correctly all the information of input file, but the MD
> simulation
> > > > started with big fluctuations of Etot in the output, and then
> died.
> > > >
> > > > other information about my previous email
> > > > 1) "533-150000" equals "533-100441" (actual number of residues of
> the
> > > > system), as the code can read in and reset the NRES;
> > > > 2) I changed cutoff=15, into es_cutoff=8.0, and vdw_cutoff=9.0,
> things
> > > > came
> > > > out the same, i.e. after 16 steps with big fluctuations in Etot,
> then
> > > > died;
> > > > 3) the starting 444K was because I set ntx=1, irest=0,ig=2858,
> ie. no
> > > > initial velocity in inte input coordinate file.
> > > > 4) the number of processors I used was 8.
> > > >
> > > >
> > > > xiaoqin
> > > > 07/20/2009
> > > >
> > > >
> > > >
> > > >
> > > > > From: rduke_at_email.unc.edu
> > > > > To: amber_at_ambermd.org
> > > > > Subject: Re: [AMBER] question of ibelly used in pmemd
> > > > > Date: Fri, 17 Jul 2009 11:48:41 -0400
> > > > >
> > > > > Okay, there is an &end on line 23 of tus1.in that I believe is
> > > > > unnecessary,
> > > > > but I don't think it is causing any problems. However I notice
> that the
> > > > > last
> > > > > entry in your "belly group" residue listing, on line 49,
> specifies
> > > > > residues
> > > > > 533-150000. That happens to be roughly 49,000 more residues
> than your
> > > > > system has... (the NRES printed out in your mdout says your
> system has
> > > > > 100,441 residues and 308,147 atoms). I would suspect that the
> group
> > > > > reading
> > > > > code in pmemd as well as sander may have a bit of trouble with
> this,
> > > > > though
> > > > > maybe I am wrong (well I looked, and it seems the code can, at
> least on
> > > > > a
> > > > > quick read, reset any excessive residue numbers to nres; I
> would still
> > > > > not
> > > > > do this) Another point, you specify a cutoff of 15 in your mdin
> for an
> > > > > ewald
> > > > > run. This should work, but has no benefit whatsoever. In
> fact, you are
> > > > > probably running about six times slower than you really need to
> because
> > > > > of
> > > > > this large cutoff, and consuming 6x as much memory in the
> pairlists.
> > > > > The
> > > > > whole idea of particle mesh ewald, the default electrostatics
> method in
> > > > > pmemd or sander, is to combine a small direct space calc (ie.,
> a short
> > > > > default direct space cutoff) with a reciprocal space calc on
> the rest of
> > > > > the
> > > > > unit cell in order to get an electrostatics calc fully
> representing the
> > > > > system with no effective cutoff, accurate to 4-5 decimal
> places, and
> > > > > more
> > > > > efficient (and accurate) than a pure cutoff system with a
> longer cutoff.
> > > > > Here, specifying a 15 angstrom cutoff, you are pretty much
> shooting
> > > > > yourself
> > > > > in the foot and wasting computer time. If you want better vdw
> numbers
> > > > > than
> > > > > provided by the 8 angstrom default, you can specify a longer
> cutoff of
> > > > > say
> > > > > 9
> > > > > angstroms; that combined with the default analytic vdw
> correction
> > > > > (vdwmeth
> > > > > 1) will give you reasonable accuracy for your vdw numbers. So
> looking
> > > > > at
> > > > > the output, you start hot (~444K) and quickly are heating
> further, I
> > > > > really
> > > > > don't know what may be wrong with the system, and would have to
> do a
> > > > > bunch
> > > > > more work with the whole system to know whether what you are
> > > > > experiencing
> > > > > is
> > > > > caused by a bad system, bad input, or a bug. Once again, what
> happens
> > > > > with
> > > > > sander? The output on group reads, nmr redirs, etc. looks
> like
> > > > > everything
> > > > > was read fine in pmemd, but I really can't be sure based on the
> info I
> > > > > have.
> > > > > I would try the smaller cutoff (just remove cut = 15 and you
> will
> > > > > default
> > > > > to
> > > > > 8) on a whim; it will greatly reduce your memory usage, and if
> you are
> > > > > running this on 8 cpu's in one box with limited memory (it is a
> big
> > > > > system),
> > > > > that could help. But I still think that given that you start
> at 444K
> > > > > for
> > > > > a
> > > > > temp, you may have a basic system problem here, that will have
> to be
> > > > > fixed
> > > > > by starting over and very carefully considering what you are
> doing.
> > > > > - Bob Duke
> > > > > ----- Original Message -----
> > > > > From: "xiaoqin huang" <xqhuang1018_at_msn.com>
> > > > > To: <amber_at_ambermd.org>
> > > > > Sent: Friday, July 17, 2009 10:54 AM
> > > > > Subject: RE: [AMBER] question of ibelly used in pmemd
> > > > >
> > > > >
> > > > >
> > > > > thanks, but I still have question about pmemd run
> > > > > here I attached again the modified input and output of pmemd
> (amber 9),
> > > > > please help me to figure out what is wrong over there.
> > > > > >From the output file, I found that the ibelly groups were read
> in, and
> > > > > >the
> > > > > >MD got started, but still something is wrong over there when
> compare
> > > > > >the
> > > > > >energy terms of the first step in output file with those in
> the output
> > > > > >of
> > > > > >sander runs for the same system.
> > > > > and after several steps, it stoped.
> > > > >
> > > > > so even the ibeely group was read in, but I donot know how it
> was
> > > > > parsed.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > > From: rduke_at_email.unc.edu
> > > > > > To: amber_at_ambermd.org
> > > > > > Subject: Re: [AMBER] question of ibelly used in pmemd
> > > > > > Date: Wed, 15 Jul 2009 17:56:00 -0400
> > > > > >
> > > > > > You have to use the group format like it says. I believe you
> need to
> > > > > > put
> > > > > > the
> > > > > > nmr redirection stuff after the last namelist, and then list
> your
> > > > > > belly
> > > > > > restraints. The *.in you gave in your earlier mail does not
> look
> > > > > > correct
> > > > > > to
> > > > > > me, in that the group input does not start with a comment
> card; you
> > > > > > may
> > > > > > have
> > > > > > to look at the doc on GROUP input again.
> > > > > > Regards - Bob Duke
> > > > > > ----- Original Message -----
> > > > > > From: "xiaoqin huang" <xqhuang1018_at_msn.com>
> > > > > > To: <amber_at_ambermd.org>
> > > > > > Sent: Wednesday, July 15, 2009 5:28 PM
> > > > > > Subject: RE: [AMBER] question of ibelly used in pmemd
> > > > > >
> > > > > >
> > > > > >
> > > > > > thanks for reply, and I tested:
> > > > > > 1) without nmropt=1, without ibelly=1, i.e. no restraints, no
> > > > > > freezing,
> > > > > > just
> > > > > > regular MD.
> > > > > > the outputs of both sander and pmemd are the same;
> > > > > > 2) with nmropt=1, but without ibelly=1, i.e. restraints, but
> no
> > > > > > freezing,
> > > > > > the restrained MD.
> > > > > > the outputs of both sander and pmemd are the same;
> > > > > > 3) with nmropt=1, with ibelly=1, i.e. restraints, and
> freezing, do
> > > > > > the
> > > > > > MD
> > > > > > again,
> > > > > > when bellymask used, the error message is:
> > > > > > "ERROR: PMEMD 9 does not support bellymask option!
> Please use
> > > > > > Amber
> > > > > > 6/7 GROUP format instead".
> > > > > > when the Amber 6/7 GROUP format is used, i.e. the input
> file I
> > > > > > attached in the previous email, the same error as described
> in my
> > > > > > previous
> > > > > > email happened.
> > > > > > -------------------------------------------------------------
> > > > > > so, how to put ibelly=1 (group list or bellymask) in the
> input file
> > > > > > that
> > > > > > can
> > > > > > be read in correctly by pmemd?
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > > From: rduke_at_email.unc.edu
> > > > > > > To: amber_at_ambermd.org
> > > > > > > Subject: Re: [AMBER] question of ibelly used in pmemd
> > > > > > > Date: Wed, 15 Jul 2009 14:22:23 -0400
> > > > > > >
> > > > > > > If you take the exact same system, run it in sander, and
> run it in
> > > > > > > pmemd,
> > > > > > > it
> > > > > > > should do the exact same thing for about 300-500 steps;
> then the
> > > > > > > systems
> > > > > > > will diverge due to rounding errors in the algorithms
> (which is of
> > > > > > > no
> > > > > > > concern - just different regions in phase space). So, is
> this what
> > > > > > > you
> > > > > > > are
> > > > > > > doing? If so, then it is likely their is some software
> installation
> > > > > > > problem
> > > > > > > or hardware problem. Did pmemd pass the amber test suite
> on your
> > > > > > > machine?
> > > > > > > It should. Okay, all that said, I looked at your mdin, and
> you have
> > > > > > > a
> > > > > > > pretty complex setup, involving both belly and nmr
> restraints.
> > > > > > > There
> > > > > > > is
> > > > > > > some possibility this is not being parsed exactly correctly
> in
> > > > > > > pmemd,
> > > > > > > but
> > > > > > > I
> > > > > > > think it is probably okay (I hardly ever use nmr
> restraints, so
> > > > > > > someone
> > > > > > > more
> > > > > > > familiar may want to look at how that is being used here).
> Looking
> > > > > > > at
> > > > > > > the
> > > > > > > output, what I see primarily is that the run goes for over
> 10 steps,
> > > > > > > but
> > > > > > > then there is an end-of-file on the restrt file; I am
> wondering if
> > > > > > > you
> > > > > > > had
> > > > > > > a
> > > > > > > hardware issue of some sort here... I would retry with
> both sander
> > > > > > > and
> > > > > > > pmemd, but for 10 steps, dumping output with each step
> (ntpr = 1),
> > > > > > > and
> > > > > > > see
> > > > > > > if there are any differences between pmemd and sander.
> > > > > > > Regards - Bob Duke
> > > > > > > ----- Original Message -----
> > > > > > > From: "xiaoqin huang" <xqhuang1018_at_msn.com>
> > > > > > > To: <amber_at_ambermd.org>
> > > > > > > Sent: Wednesday, July 15, 2009 1:34 PM
> > > > > > > Subject: [AMBER] question of ibelly used in pmemd
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Hi, users,
> > > > > > > I have a question about ibelly=1 used in pmemd simulations.
> > > > > > > the situation is that I want to freeze some part of
> residues/atoms
> > > > > > > of
> > > > > > > the
> > > > > > > system, so I used the ibelly=1 in the sander, it works well
> no
> > > > > > > matter
> > > > > > > which
> > > > > > > version (8, 9, 10).
> > > > > > > when I used the same ibelly=1 in the pmemd (amber 9), the
> MD runs
> > > > > > > and
> > > > > > > then
> > > > > > > stopped with the message as vlimit exceeded for step 1...
> > > > > > > here attached is the input file, output file and the error
> message.
> > > > > > > any suggestions or comments? thanks!
> > > > > > >
> > > > > > > xiaoqin
> > > > > > >
> > > > > > > 09/15/2009
> > > > > > >
> > > > > >
> > > > > >
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> > Windows LiveT HotmailR: Celebrate the moment with your favorite
> sports pics. Check it out.
> >
> http://www.windowslive.com/Online/Hotmail/Campaign/QuickAdd?ocid=TXT_TA
> GLM_WL_QA_HM_sports_photos_072009&cat=sports___________________________
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> _________________________________________________________________
> Windows LiveT HotmailR: Search, add, and share the web's latest sports
> videos. Check it out.
> http://www.windowslive.com/Online/Hotmail/Campaign/QuickAdd?ocid=TXT_TA
> GLM_WL_QA_HM_sports_videos_072009&cat=sports___________________________
> ____________________
> AMBER mailing list
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