[gmx-users] Re: Energy Minimization

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 12 08:54:24 CET 2005

On Tue, 2005-01-11 at 16:42 -0800, Gia Maisuradze wrote:
> Hi,
> I am a new user of GROMACS. I have sent this message one week ago but
> did not get any answer. I am trying to run MD simulation of one of the
> proteins. I followed the "getting started" tutorial. My question is
> about minimization of my system in solvent. According to the tutorial
> the minimization should be finished when either the minimization has
> converged or a fixed number of steps has been performed. In my case
> the minimization has converged before it reached the fixed number of
> steps. But the potential energy after minimization IS NOT lower than
> potential energy calculated by formula: -42(kJ/mole)xN (N is a number
> of SPC water molecules). What is the problem? How can I fix it? The
> same problem I had for Ribonuclease S-peptide given in tutorial. As I
> heard the problem might be a precision. Am I correct? My calculations
> run in single precision, so I may need a double precision. But I don't
> know how to change the precision. Can anyone help me to change a
> single precission to double precision? Is there any other ways to fix
> this problem? 
Is the number of waters correct? It is not in the tutorial.
> My second question is about short and full MD run. According to the
> tutorial to generate the input for the position restrained mdrun we
> have the following command:
> grompp -f pr -o pr -c after_em -r after_em -p speptide
> for full md to do the same thing we have the following command:
> grompp -v -f full -o full -c after_pr -p speptide
> We can see that full MD is quite similar to the restrained MD, but
> there is a difference which makes impossible to run full MD without
> restrained MD. In full MD we have "-c after_pr" which is an input file
> and "after_pr" can be obtained from short MD run. Is it correct that
> we can't run full MD run without short MD or is there any other way to
> run directly full MD (for example, use the same files for full MD as
> used for short MD)?
If you don't do the PR you may end up with large forces due to the newly
added solvent which may disrupt your original structure. This is usually
not what you want, but that is for you to decide of course.
> I look forward to hearing your reply,
> With best wishes,
> Gia Maisuradze  
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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