[gmx-users] restarting a sorted shuffled trajectory

Alan Dodd anoddlad at yahoo.com
Mon Feb 12 19:05:29 CET 2007

>From memory, deshuffling, followed by using editconf to change confout.gro to a pdb and back again, results in the molecule types all being in the same order again (in my case, protein, lipid, solvent, ions instead of protein, lipid, ions, water, lipid, ions, water, lipid, ions, water, protein etc).  Actually... I think ions might move about, but this process at leasts put them all in the same place, even if you then have to check which order the groups are in.  I couldn't say for certain if the molecules within a set group stay in the same order, but this can at least let you use the same .top with minimal or no alterations.

----- Original Message ----
From: Stéphane Téletchéa <steletch at jouy.inra.fr>
To: gmx-users at gromacs.org
Sent: Monday, February 12, 2007 5:00:24 PM
Subject: [gmx-users] restarting a sorted shuffled trajectory

Dear all,

I'm willing to do a fine-tuning start for my simulation using multiples 
prX.mdp input.

I'm launching the first run using -shuffle -sort from grompp (with 
pr1.mdp), but i'd like to know how to reuse the resulting .trr file for 
the second pr (pr2.mdp).
I've tried deshuffling first the trr file but do i also need to desort 
it ? (as Chris Neale posted on 24.01.2007 on this list)

So far, i'm getting:

Warning: atom names in ../test_min_deflated26_sol_ions.top and 
../toto_min_formd.gro don't match (HW2 - HW1)
(more than 20 non-matching atom names)
WARNING 1 [file "../test_min_deflated26_sol_ions.top", line 38]:
   23642 non-matching atom names
   atom names from ../test_min_deflated26_sol_ions.top will be used
   atom names from ../OR1G1_min_formd.gro will be ignored

The mdrun was launched after this grompp input :

grompp_lam \
     -f mdp/md_Na.mdp \
     -p test_min_deflated26_sol_ions.top \
     -pp test_min_deflated26_sol_ions_out.top \
     -c toto_min_formd.gro \
     -o fullmd_ions.tpr \
     -po md_Na_out.mdp \
     -deshuf fullmd_ions.ndx \
     -shuffle \
     -sort \
     -np 4

I'd like to pursue the dynamics, so far i'm doing:

cd test
grompp_lam \
     -f ../mdp/pr1.mdp \
     -p ../test_min_deflated26_sol_ions.top \
     -pp test_out.top \
     -c ../toto_min_formd.gro \
     -t ../fullmd_ions_deshuf.trr \
     -e ../fullmd_ions.edr \
     -n  toto_min_formd.ndx \
     -o test.tpr \
     -po test_out.mdp \
     -np 4

Thanks a lot for your comments/advices.



Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901
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