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 - 09:42:15 CDT

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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