Stefano Meliga wrote:
Hi again,
I've tryed to perform the same preprocessing and EM steps without
distance constraints and the situation improves a lot.
I get no warnings in the steepest descent EM and only one molecule
cannot be set in the conjugate gradient EM.
Can you see the reason?
Were you constraining bond lengths or using position restraints? You've
combined the terminology (restraints and constraints are separate ideas in Gromacs).
LINCS warnings and related problems are discussed extensively in the list
archive (with potential solutions!) as well as on the wiki:
http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
If the problem arises only after adding ions, inspect the location of ion
insertion. Since it is random, ions may have been placed in an unfavorable
location, causing them (or a nearby water molecule) to go careening through the
simulation cell. That happened to me once :)
-Justin
Thanks,
Stefano.
Stefano Meliga ha scritto:
Hi everybody,
I neutralized my system with the commands:
$grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p
4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
$grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname
CL-
(adding the atoms to the solution SOL)
I renamed the files to keep track of the different topology files:
mv 4AKEallHsol_pre.top 4AKEallHion.top
mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top
I run an all-bonds position restraint steepest descent EM:
$grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
4AKEallHion.tpr
$grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v
mdrun exits successfully but displays the warning:
t = 0.011 ps: Water molecule starting at atom 17223 can not be settled.
Check for bad contacts and/or reduce the timestep.
In the gro file atom 17223 is an oxigen of the solution
Going further with my simulation i run a all-bonds position restrained
conjugate gradient EM:
$grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top
-o 4AKEallH_PREMsteep.tpr
$grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v
but get the fatal error:
Source code file: constr.c, line: 136
Fatal error:
Too many LINCS warnings (2200)
And some of this warnings are again solution's molecules that cannot
be set.
May the problem be related to the ions added to neutralise the system?
mdrun was not showing this problem with the non-neutral system in
input.
Thanks a lot,
Stefano
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
