Stefano Meliga wrote:
My integrator is "steep", which should perform EM.
This is my mdp file:
title = 4AKE_PREMsteep
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = all-bonds
integrator = steep
nsteps = 500
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
DispCorr = no
;
; Energy minimizing stuff
;
emtol = 1.0
emstep = 0.01
I learnt from the tutorials (s-peptide) that in order to do a position
restrained MD the I have to set the constraints (all-bonds in this case).
Is that incorrect? Is it valid for EM as well?
Position restraints != bond contraints. Using "constraints = all-bonds" will
constrain the bond lengths, but not restrain the positions of the atoms.
If you want to do position-restrained MD, you have to "define = -DPOSRES"
(according to the #ifdef POSRES block in the topology, assuming you made one
automatically from pdb2gmx). Using position restraints in EM doesn't serve much
of a purpose in my mind, unless you really need to preserve the exact initial
configuration; it may in fact prevent your system from converging if some bad
geometry is being held in place.
-Justin
Thank you for your advice,
Stefano.
Mark Abraham ha scritto:
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?
Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your
integrator in your .mdp file better.
Also, as Justin suggests, please be careful with the
constraint/restraint terminology.
Mark
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
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--
========================================
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
========================================
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