On 4/19/13 11:55 AM, Shima Arasteh wrote:
All right.
And if minimization doesnt fix such a problem, what would be the solution?
However I have not tried it on my own system yet.
It's a waste of time to delve into hypotheticals. Please try the advice you've
been given and report back if needed. Crashes like you are seeing are almost
invariably due to poor starting configuration. Thorough EM solves that problem.
If, for some reason, that doesn't work, we will continue to diagnose.
-Justin
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Cc:
Sent: Friday, April 19, 2013 8:22 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:43 AM, Shima Arasteh wrote:
Thanks for your reply.
I' d like to know if I need to remove all position restraints before
MDRUN?means that the last step of npt should be done without position
restraints?
Whatever makes sense for your system. There is no universal answer to how
equilibration should be done. If your simulation is crashing at step zero, I
doubt that removing restraints will help in any way.
-Justin
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Cc:
Sent: Friday, April 19, 2013 7:58 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:26 AM, Shima Arasteh wrote:
Hi,
I tried to equilibrate my system by setting timestep=1 fts and decreasing the
position restraints step by step.
But when I go to MDRUN step, it doesnt work and some pdb files are printed.
what is printed in my log file is as follow:
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
8.34161e+04 5.57602e+04 7.65365e+02 -1.97155e+02 8.52248e+03
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
-1.06644e+05 8.46716e+04 -5.77343e+03 -1.11612e+06 -2.67240e+05
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-1.26284e+06 6.13687e+05 -6.49154e+05 8.17667e+02 -1.08370e+02
Pressure (bar) Constr. rmsd
-8.62031e+04 5.99322e-04
Would you please give me any suggestions? Does my system need more
equilibration yet? longer equilibration time?
Whats the problem? My settings as sent you earlier seem fine, so whats the
solution?
Thanks for your suggestions. They would be appreciated.
The temperature is 817 K, indicating something is moving with a ridiculously
high velocity that has been imparted by strong forces. You have atoms
overlapping somewhere. Try more thorough energy minimization.
-Justin
Sincerely,
Shima
________________________________
From: Justin Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Sunday, April 7, 2013 4:46 PM
Subject: Re: [gmx-users] unstable system
On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh <shima_arasteh2...@yahoo.com>
wrote:
Hi all,
I have a system of peptide/POPC/water/ions. The energy minimization and
NVT steps has passed successfully. I ran NPT step for around 10 ns with
restraints of protein and P atoms at first nano seconds and then removing them
gradually.
I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they
are still restrained. When I run the mdrun command, I get error of "X particles
communicated to PME node Y are more than a cell length out of the domain decomposition
cell of their charge group" .
I know this error means an unstable system. When I visualized the written pdb
files, I see some popc hydrogen atoms are broken and located between two
leaflets which are separated by a gap. The protein seems ok, however I don't
get many pdb files to see.
As what I see in Diagnosing unstable system web page,
1. it would be beneficial if one see what part of the system is unstable in first steps.
As I saw, the unstable "POPC hydrogen atoms" are not fine.
2. The single molecules are supposed to examine in water or vacuum too. I have
passed this step successfully.
3. I have not ignored any warning during the last steps.
4. And my mdp files to run md is as follow:
integrator = md
dt = 0.002
nsteps = 5000000
ns_type = grid
nstlist = 5
rlist = 1.2
rlistlong = 1.4
rcoulomb = 1.2
rvdw = 1.2
pbc = xyz
vdwtype = switch
rvdw_switch = 1.0
What force field are you using? CHARMM? In any case, the value of rvdw_switch
does not make any sense. If you're using CHARMM, it should be 1.0.
; Parameters for treating bonded interactions
continuation = yes
constraint_algorithm = LINCS NCS / SHAKE)
constraints = all-bonds )
lincs_iter = 1
lincs_order = 4
; Parameters for treating electrostatic interactions
coulombtype = PME ; Long range electrostatic interactions treatment
(cut-off, Ewald, PME)
pme_order = 4 ; Interpolation order for PME (cubic interpolation is
represented by 4)
fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME
(nm)
; Temperature coupling parameters
tcoupl = Nose-Hoover
tc-grps = Protein_POPC Water_and_ions ; Define groups to be
coupled separately to temperature bath
tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps)
ref_t = 310 310 ; Group-wise reference temperature (K)
; Pressure coupling parameters
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 2.0
ref_p = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5
; Miscellaneous control parameters
; Dispersion correction
DispCorr = EnerPres
; Initial Velocity Generation
gen_vel = no
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm = 1 y (steps)
comm_mode = Linear
comm_grps =Protein_POPC Water_and_ions ; COM removal relative to the
specified groups
Would you please let me know if these happen due to an improper
equilibration? Do I need to extend the NPT step? Would that fix it?
Aside from the above comment, there is nothing particularly wrong about the
.mdp file aside from some odd characters here and there, which I will assume
are nothing more than quirks of transferring to an email, as they otherwise
would have triggered fatal errors in grompp.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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