[gmx-users] shell molecular dynamics

[michael zhenin]

Hello,

I would like to run a simulation using the shell option.

I tried to restraint solvent molecules which were found within the range
of 5-10 angstroms from the box center. I couldn't find any way to do
so. I didn't find any information about this topic anywhere else
i.e. GROMACS manual, online tutorials etc.

Can anybody help me with this problem or guide me to appropriate tutorial.

Thanks in advance.

Michael
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] Questions regarding REMD simulation

[michael zhenin]

Hi All,

I have few questions regarding REMD simulation.

I assume REMD works in the following way: Each replica starts with a given
temperature and the temperature of each replica changes along the simulation
(as described in Sugita and Okamoto publication, 1999). Then demux.pl and
trjcat collect the trajectories of the lowest temperature from each replica.



My problem is that while analyzing the results, I found in the edr
files that the temperatures along each replica are relatively

constant (+- 2K from the starting temperature) and the average temperature
is equal to the initial temperature.


How can this be explained? Does the temperature of each replica change
along the simulation or maybe the temperature of each

simulation stays close to its initial value and the coordinates are changed
between the different replica? (if so, why do i need to use

the post-processing tools such as the demux.pl script?)


Thanks,


Michael
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] mdrun

[michael zhenin]

Dear all,
I am trying to run dynamics (mdrun) on GROMACS 4.5.3 in parallel on 8
processors, but it crashes after a while and refuses to reach to the end.
The error note that pops out is:

1 particles communicated to PME node 4 are more than 2/3 times the cut-off

 out of the domain decomposition cell of their charge group in dimension
y.

 This usually means that your system is not well equilibrated


My system contains protein, ATP and Mg. I have equilibirated it for 300 ps
that were divided into 3 parts.
The first 2 parts were the NVT equilibiration (the first one was made in
order to equilibrate only the water) - 100 ps each.


The third was the NPT - 100 ps.
The system wasn't constraint.

My mdp file is :

title = OPLS wt nbd1 MD
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 2000 ; 1 * 2000 = 2 ps, 20 ns


dt = 0.001 ; 1 fs
; Output control
nstxout = 2 ; save coordinates every 2 ps
nstvout = 2 ; save velocities every 2 ps
nstxtcout = 2 ; xtc compressed trajectory output every 2 ps
nstenergy = 2 ; save energies every 2 ps


nstlog = 2 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)


rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
ewald_rtol = 1e-05


fourierspacing = 0.12 ; grid spacing for FFT
pme_order = 6 ;
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate


tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors


tau_p = 1.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC

; Dispersion correction

DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
morse = yes


I've searched the net for this error and didn't find any answer. Did anybody
see this error? and what should i do with it..

Thanks,

Michael
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists