AMBER Archive (2009)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Jul 20 2009 - 12:10:03 CDT

Hi Kristina,
Thanks much for your assistance with this stuff now (as well as in the past,
if memory serves). If I get the actual inputs, I will be able to do some
testing myself. At least in my experience, the grief tends to come from the
order of reading different sections. PMEMD is pretty flexible about finding
all the namelists, but the other stuff has to be in a specific order, and
unfortunately that order may not be consistent with sander (I remember
falling into a bit of a code modification swamp on this, trying to reproduce
both the mdout output and the reading order for extra functionality of this
sort - but I thought we had it all working acceptably). I don't think this
was particularly well documented in sander in the past, and not documented
in pmemd; once we figure out what is being read though, we will hopefully be
good. I unfortunately have never taken the time to move the
bellymask/restraintmask code over to pmemd; that would probably help too.
Thanks again - Bob
----- Original Message -----
From: "Kristina Furse" <Kristina.Furse.1_at_nd.edu>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Monday, July 20, 2009 12:56 PM
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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