AMBER Archive (2009)
Subject: RE: [AMBER] trajout problem
From: Anna Reymer (reymer_at_chalmers.se)
Date: Mon Nov 30 2009 - 06:58:39 CST
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
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.
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.
> Anna Reymer, PhD student
> Physical Chemistry,
> Department of Chemical and Biological Engineering
> Chalmers University of Technology
> Kemivägen 10
> SE-412 96 Gothenburg
> Phone: +46-(0)31-7722815
> AMBER mailing list
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