[gmx-users] restarting a sorted shuffled trajectory

[Yang Ye]

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 <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.
>
> Cheers,
>
> Stéphane
>
>