[gmx-users] re:MDP options for CCL4 solvent

PeiQuan Chen gromacs at 163.com
Thu May 29 12:13:01 CEST 2003

Dear gmx-users:

>I am doing a Simulation of a lipase (1CRL) in ccl4 solvent. I 
>would like to know how i go about editing the options in the mdp 
>file. I am preparing the mdrun using the following commands

>1. pdb2gmx -f 1CRL -p crl.top -o crl.gro -n index.ndx -i crl.itp
>2. editconf -f crl.gro -o crlconf -d 1 -c
>3. genbox -cp crlconf -cs ccl4_box -o crlbox
>4. grompp -f ccl4.mdp -o crlmpp -p crl -c crlbox -np 16

>when i do the mdrun i get an error in PBC. I would like to know 
>how do i set the options in the mdp file for different solvents 
>and different proteins.
   I have uploaded three opls rigid model solvent boxs to gromacs topologies(CCl4 CHCl3 CH2Cl2) sites.
You can download it and look it up how to setup the mdp files.
   The ccl4 box I made can reproduce the density and Dvap of experiment within 1%.
   Ps: The solvent boxes is just a test. They maybe have bugs. The boxes is suitable using oplsaa force field,
and It can be used in other force field. Just change the sigma and epsilon paraterments to C6 and C12.

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	

More information about the gromacs.org_gmx-users mailing list