[gmx-users] Question about CCl4 box!
gromacs at 163.com
Fri May 2 18:49:00 CEST 2003
Dear David :
I have followed your instruction to make my cubic box vetor from 32.59nm to 4.35nm.But the problem don't resovle
yet. I can only use the tau_p=5.0 or > 5.0 and the constraint_algorithm can only use the shake not can use lincs.
If I change the value. My simulation will be carsh after generate a series *step* files.
Ps:I can well reproduce the Experiment data of DHvap and density in such conditions.
I want to ask that whether tau_p=5.0 is a resonable value to simutions.
The following this my .mdp file:
;MD at 300K
;Total simulation time: 3000 ps
cpp = /lib/cpp
;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator = md
:time step in femtoseconds
dt = 0.001
;number of steps
nsteps = 3000000
;frequency to write coordinates to output trajectory file
nstcomm = 1 ; reset c.o.m. motion
nstxout = 10000
;frequency to write velocities to output trajectory file
nstvout = 10000
;frequency to write energies to log file
nstlog = 5000
;frequency to write energies to energy file
nstenergy = 500
;group(s) to write to energy file
energygrps = System
;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist = 5
ns_type = grid
;cut-off distance for the short-range neighbor list
;treatment of electrostatic interactions
coulombtype = Cut-off
;treatment of van der waals interactions
vdwtype = Cut-off
dispcorr = EnerPres
tcoupl = berendsen
tc-grps = System
tau_t = 0.1
ref_t = 300
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 173529
constraints = none
constraint_algorithm = shake
shake_tor = 0.0001
rlist = 0.8
rcoulomb = 1.4
rvdw = 1.4
>On Thu, 2003-04-24 at 15:06, PeiQuan Chen wrote:
>> Dear David van der Spoel:
>> I have chage the vdwtype = cut-off and rvdw switch to 0.
>> But the program told me that:
>> Fatal error: One of the box vectors has become shorter than twice the cut-off length.
>OK, make your box larger or your cutoff shorter, check density when it
PeiQuan Chen Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone: (86)2223506728 Mobile Phone: (+86)13920675030
gromacs at 163.com
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