Subject: Re: [gmx-users] Help!!!!!
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Wed Oct 16 11:39:51 CEST 2002
On Wed, 16 Oct 2002, Dmitry Kovalsky wrote:
> > 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?
because output.gro doesn't have high precision. One doesn't need
velocities while doing minimization.
In any case, I suggest you should use double precision to get really good
> Sincerely yours,
> Ph.D. Student Dmitry Kovalsky
> Institute of Molecular Biology & Genetics
> 150 Akad. Zabolotnogo Street,
> Kiev-143, 03143
> E-mail: dikov at imbg.org.ua
> Fax: +380 (44) 266-0759
> Tel.: +380 (44) 266-5589
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