On Jun 1, 2009, at 1:12 PM, Stefano Meliga wrote:
Hi again,
The energy minimization with conjugate gradient integrator still
gives me two warnings of the type:
t = 0.011 ps: Water molecule starting at atom 28122 can not be
settled.
Check for bad contacts and/or reduce the timestep.
My command lines are:
$grxdir/grompp -f 4AKEpreEMcg.mdp -po 4AKE_EMcg.mdp -c
4AKE_EMsteep.gro -p 4AKEallHion.top -pp 4AKEpreEMsteep.top -o
4AKE_EMcg.tpr
$grxdir/mdrun -s 4AKE_EMcg.tpr -o 4AKE_EMcg.trr -c 4AKE_EMcg.gro -e
4AKE_EMcg.edr -g 4AKE_EMcg.log -v
This is my mdp file 4AKEpreEMcg.mdp:
title = 4AKE_EMcg
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = none
integrator = cg
nsteps = 1500
nstlist = 50
change that to 1
if it does not get better it means that your system is build in such a
way that you have bad contacts
that the minimization can not remove. You have to check where there
are and do something about it.
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
; Energy minimizing stuff
;
emtol = 1.0
emstep = 0.01
The minimization is successful but I don't see the meaning of this
timestep.
Thanks,
Stefano.
Justin A. Lemkul ha scritto:
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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