AMBER Archive (2009)

Subject: Re: [AMBER] trajout problem

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Nov 30 2009 - 07:56:43 CST

try simplifying the run- make it single cpu and only run for 1 step. maybe
you'll get more info in your mdout file.
are you running interactively or submitting to a queue? maybe the queue
output/error file has info. it sounds like you might be getting an error
reading the restart file but it isn't creating an output.

On Mon, Nov 30, 2009 at 7:58 AM, Anna Reymer <reymer_at_chalmers.se> wrote:

> Thanks a lot Carlos for your quick response.
>
> Well, I do have periodic box. I tried 'nobox' option just to see whether it
> will produce something else. Initially I was not using 'nobox', however the
> rst file produced then and gave no output with sander as well.
>
> The input file is the following:
>
> GCGAATTGCG + Ru_phen2_dppz: 1ns MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 500000, dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
>
>
> And yes, I am using the same topology file and the same mdin file as I used
> to generate the previous trajectories.
>
> Thanks again for help.
>
> /Anna
> ________________________________________
> From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of
> Carlos Simmerling [carlos.simmerling_at_gmail.com]
> Sent: Monday, November 30, 2009 1:09 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] trajout problem
>
> the second half is velocities, and since there are none in the trajectory
> file, ptraj just adds zeros. this should not cause sander to get stuck
> though, just means the velocities are zero.
> it's hard to know what's wrong with the little information you have given.
> is the system periodic? I assume no, since you say "nobox". what is your
> input file? are you using the same setup as the one used to generate the
> trajectory file? (meaning same prmtop, same mdin file)
>
>
>
> On Mon, Nov 30, 2009 at 7:03 AM, Anna Reymer <reymer_at_chalmers.se> wrote:
>
> > Dear All,
> > I have the following problem.
> > When I try to run MD where I use my complex.rst as an input coordinates
> > file and Sander produces no output files, neither trajectory file, nor
> > restart file and the out file is just empty.
> >
> > I have tested the input and topology files and they are fine, and the
> > problem seems to be in the restart file.
> >
> > I produce the restart file from a trajectory file, using ptraj script:
> >
> > trajin md_2_complex.mdcrd 4243 4243
> > trajout complex.rst restart nobox append
> >
> > I guess the problem is in initial rst file, which, for some strange
> reason,
> > contains just columns of zeroes in the second half.
> >
> > Has anybody any advice? Thanks in advance.
> >
> > Regards,
> > Anna
> >
> > -----------
> > Anna Reymer, PhD student
> > Physical Chemistry,
> > Department of Chemical and Biological Engineering
> > Chalmers University of Technology
> > Kemivägen 10
> > SE-412 96 Gothenburg
> > Sweden
> >
> > Phone: +46-(0)31-7722815
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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