[gmx-users] Question about CCl4 box!

PeiQuan Chen 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
;Temperature coupling
tcoupl  		 = berendsen
tc-grps 		 = System    
tau_t			 = 0.1    
ref_t			 = 300  
;Pressure coupling
pcoupl  		 = berendsen
pcoupltype		 = isotropic
tau_p			 = 5
compressibility 	 = 4.5e-5
ref_p			 = 1.0
;Velocity generation
gen_vel 		 = yes
gen_temp                 = 300
gen_seed                 = 173529

;No constraints
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

Sincerely yours
PeiQuan Chen
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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