[gmx-users] RB dihedral again and dihedral constants
spoel at xray.bmc.uu.se
Tue Apr 15 11:37:01 CEST 2003
On Tue, 2003-04-15 at 10:55, nanyu101 wrote:
> Dear Dr.David,
> Thanks for your prompt reply.I have known there are many parameters for RB dihedral type in OPLS.But if I want to simulate my system in ffG43a2 force field, where should I put these force constants that I have already fitted them ourselves.
> By the way,I have met something very interesting when I try to understand how the torsion parameters work. I have done as follows:
> 1.I have changed all the dihedral force constants to zero and run energy minimization of my system,the Gromacs give me the same results as before I have changed the dihedral force constant. Do you know what has happened?
> 2.Firstly,I think that Gromacs has not read ffG43a2bond.itp file,so I have change one bond constant to zero,the result changed.Now,we can conclude that Gromacs has read ffG43a2bond.itp file,but why didn't it read the dihedral part?
> Do Gromacs do some special operation when the force constant is zero?
> Thanks for your help and any comment is appreciated.
try to check whether your tpr file really has changed before and after
(use gmxcheck -s1 -s2)
Otherwise (if the energies really are identical) it may be that your
molecule is in the dihidral minimum energy already.
> Best wishes,
> Xianhui Wu
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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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