Dongsheng Zhang wrote:
On Thu, 2006-09-14 at 06:36 -0700, David van der Spoel wrote:
Navratna Vajpai wrote:
Hi all..
I wrote this mail yesterday. But could not receive any reply till now.
So if someone can suggest something about it. That would be nice.
Best regards
Nav
Begin forwarded message:
*From: *Navratna Vajpai [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
*Date: *September 13, 2006 10:32:21 AM GMT+02:00
*To: *Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
*Subject: **[gmx-users] Hi...*
*Reply-To: *Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
Dear All
Hi..
This is in regard to your previously replied mail regarding the use of
GROMOS96 or OPLS-AA or AMBER force field.
As you said it depends upon the users taste which one to use. This
means that the three on a broad manner should give convergence of
the analyzed data set.
Infact from my simulation runs using oplss-aa and gromos96, I didn't
found that. I tried using the GROMOS96 and opls-aa force field on my
small peptides for a period of 20ns and found that with opls-aa even
the phi-psi combination of the individual amino acids were incorrect.
Actually this always puzzled me to make a choice for the Force field.
The rest of the script was unchanged for the two runs.
Could you please comment on the above results? Is there any way really
to judge which force field is to be chosen for particular type of
analysis?
Best regards
Nav
what do you mean with incorrect? your question is quite vague.
the g_rama program works only for GROMOS like force fields unfortunately
but that doesn't mean the phi/psi are wrong.
Could you please give more detail why g_rama program works only for
GROMOS like force field? To my understanding, the reason to get
different values of phi/psi by using g_rama or g_angle is that the
definition of phi/psi in g_rama is not in a conventional way. If we
define phi/psi in the same way as g_rama, I believe g_angle will give
the same answer. No matter which force field is used, these two methods
will give different values. Is my understanding correct?
because atom names are hardcoded. if you give g_angle the right
definitions in the index file it will work correctly.
All the best!
Dongsheng
What would be the correct
result anyway? Maybe your peptide unfolds.
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--
David.
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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