Subject: Re: [gmx-users] Help!!!!!

Dmitry Kovalsky dikov at
Wed Oct 16 11:19:46 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 ?
> you should use : grompp with the option -t *.trr where *.trr is the file
> obtained by the steepest descent minimization.

But why it doesn't work if to use simply ouput.gro  from previous steepest 
descent, without -t option? As I undersand output.gro should contain 
velocities also? Or I have missed something?

Sincerely yours,


Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143

E-mail: dikov at
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589

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