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Dear GROMACS users,<br>
<br>
While running a simple MD simulation with both a small protein such as
BPTI and a larger one such as tmRBP_Unliganded_2FN9.pdb, I'm
encountering an odd situation in which one (in the case of BPTI) or
several Calphas (in the later case) are "detaching them selfs" from the
main group. <br>
The problem appeared only after adding salt to the simulation(at least
in the case of BPTI).<br>
I would appreciate any suggestions and comments on the matter.<br>
<br>
Thanks <br>
<br>
Arik<br>
<br>
The run files are:<br>
<br>
<b>em.mdp:</b><br>
<br>
title = tmRBP_Unliganded_2FN9 Minimization<br>
integrator = steep ; (steep)using steepest descent<br>
nsteps = 50000<br>
nstlist = 1<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb = 1.0<br>
vdw-type = cut-off<br>
rvdw = 1.0<br>
nstenergy = 10<br>
emtol = 5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0<br>
<br>
<br>
<b>pr.mdp<br>
</b><br>
title = tmRBP_Unliganded_2FN9 PR<br>
integrator = md<br>
nsteps = 50000<br>
dt = 0.002 ;(in ps) doing a 100ps traj.<br>
constraints = all-bonds<br>
nstlist = 10 ; neighbour list updates every number of steps<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb = 1.0<br>
vdw-type = cut-off<br>
rvdw = 1.0<br>
tcoupl = Berendsen<br>
tc-grps = Protein non-protein<br>
tau-t = 0.1 0.1<br>
ref-t = 298 298<br>
Pcoupl = Berendsen<br>
tau-p = 1.0<br>
compressibility = 5e-5 5e-5 5e-5 0 0 0<br>
ref-p = 1.0<br>
nstenergy = 100<br>
define = -DPOSRES ; include posre.itp(position restraint)
file<br>
<br>
<b>run.md<br>
</b>title = tmRBP_Unliganded_2FN9<br>
integrator = md<br>
nsteps = 300000<br>
dt = 0.001<br>
constraints = all-bonds<br>
nstlist = 10<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb = 1.0<br>
vdw-type = cut-off<br>
rvdw = 1.0<br>
tcoupl = V-rescale ;V-rescale<br>
tc-grps = Protein non-protein<br>
tau-t = 0.8 0.8<br>
ref-t = 298 298<br>
nstxout = 1000<br>
nstvout = 1000<br>
nstxtcout = 1000<br>
nstenergy = 1000<br>
<br>
<br>
<br>
The runs commands are(integrated inside a C++ code):<br>
<br>
SysCommand1 = "echo 6 | pdb2gmx -f " + FileName + " -water tip3p";<br>
<br>
system("editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro");<br>
<br>
system("genbox -cp box.gro -cs spc216.gro -p topol.top -o
solvated.gro");<br>
<br>
<br>
minimization:<br>
-------- <br>
if(Mode == "NoSalt")<br>
{<br>
system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o
em.tpr");<br>
<br>
//system("mpirun -np 4 mdrun -v -deffnm em"); <br>
}<br>
if(Mode == "WithSalt")<br>
{<br>
system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o
em.tpr");<br>
<br>
system("mpirun -np 4 mdrun -v -deffnm em"); <br>
}<br>
<br>
<br>
Salting:<br>
--------<br>
system("echo 12 | genion -s em.tpr -conc 0.1 -neutral -o
solvated.gro");<br>
<br>
pr:<br>
---- <br>
system("grompp -f MDP/prmd.mdp -p topol.top -c em.gro -o pr.tpr");<br>
/* The actual run*/<br>
system("mpirun -np 4 mdrun -v -deffnm pr"); <br>
<br>
<br>
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