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
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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