No. You don't need to "desort" it.
But from your error message, it seems not related to "shuffling and
sorting" but between your .top and .gro.
Did you "deshuffle" toto_min_formd.gro? Can you check your .top and .gro
more carefully?
Regards,
Yang Ye
On 2/13/2007 2:05 AM, Alan Dodd wrote:
>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 <[EMAIL PROTECTED]>
To: gmx-users@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.
Cheers,
Stéphane
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