[gmx-users] MDP options for CCL4 solvent

[David]

On Thu, 2003-05-29 at 09:11, Venkat Ramanan K wrote:
> Hi all,
> 
> 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.
there is no fundamental difference between ccl4 and water. PBS errors
come in many flavors, most likely is poor starting conformation. (see
mails about genbox)
> 
> thanks a lot
> 
> Venky
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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