There are several potential problems all combined into one. As has been
reported on the list, applying freezegrps, constraints, and pressure coupling
all at the same time do not mix well. The best bet is to turn off the pressure
coupling if you're set on using freezegrps. Otherwise, use position restraints
if you require NPT.
-Justin
vivek sharma wrote:
Hi justin,
thanks for your response.....
following is the .mdp file pasted..
_____
title = trp_drg
warnings = 10
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 2500000 ; total 5000.0 ps.
nstcomm = 1
nstxout = 25000 ; output coordinates every 0.5 ps
nstvout = 100000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
energygrps_excl = freeze freeze freeze SOL ! To remove
computation of interactions between the frozen groups with surroundings (i.e. the solvent, SOL)
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1
tc_grps = protein sol NDP
ref_t = 300 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Non-equilibrium MD stuff
freezegrps = freeze
freezedim = Y Y Y
____
With Thanks,
Vivek
2008/10/17 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
vivek sharma wrote:
Hi Tehre,
i am running a job by keeping a part of molecule freeze ....by
using the .mdp option....
What is your entire .mdp file?
-Justin
______________
________
energygrps_excl = Terminal Terminal Terminal SOL ! To
remove
computation of nonbonding interactions between the frozen groups
with each other
and surroundings (i.e. the solvent, SOL)
freezegrps = Terminal ! Index group to freeze
freezedim = Y Y Y ! Freeze this group in all
directions, x,
y, and z
___________________________________________________
where frreze is a group mentioned in the index file...
During the run the job is being terminated with the following error
.
__________________________________________________________
Step 1 Warning: pressure scaling more than 1%, mu: -3.51079e+22
-3.51079e+22 -3.51079e+22
-------------------------------------------------------
Program mdrun_d, VERSION 3.3.3
Source code file: ns.c, line: 258
Fatal error:
Box was shifted at least 10 times. Please see log-file.
-------------------------------------------------------
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_d on CPU 0 out of 24
srun: error: n216: task0: Aborted
srun: Terminating job
__________________________________________________________________
Can somebody give an insight in the problem for figuring out the
probable cause of the error.
PS::Before the run I mentioned the boxsize in editconf as "-box
7.5 5 6 ", to keep the size of box and number of solvent optimum.
Does it have anything to do with the mentioned error ?
Looking for suggestions..
with thanks,
Vivek
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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