[gmx-users] Help!!!!!

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 15 17:06:25 CEST 2002

On Tue, 15 Oct 2002, Tanos wrote:

>  Dear Users, 
>  I am a phD student trying to use GROMACS to minimize a large protein 
>structure. I have already arrived the emtol of 418 Kj/mol.nm with steepest 
>descent and I would like to continue the minimization with cg using the 
>final structure of the previous calculation as starting point. I have noted 
>that if I simply use grompp, GROMACS will ignore the previous results and 
>start from the non minimized struture. 
>  How should I proceed to make this work ? Is there in GROMACS any program 
>that does it ? All I want is to do a minimization starting with the results 
>of a previous one. Could someone help me ?
if you do a mdrun it will output a file called (by default) confout.gro
this you have to feed into grompp for the next round of minimization.

Your energy should definitely be negative...

>  Best whises, 
>  Tanos Celmar Costa Franca 
>  phD student 

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 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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