Shankar Prasad Kanaujia wrote:
Dear justin,
sorry for writing person mail.
I am attaching the .mdp file.
You are using a shift potential for vdwtype (and you haven't applied it
correctly - read the manual.) Therefore, LJ terms are cut off at rvdw (the LJ
term is zero beyond this point) and you are not seeing a long-range LJ term.
Using PME for coulombtype means that the "long range" component of the
electrostatic nonbonded energy is in Coul.-recip.
-Justin
thanking you.
--
Yours Sincerely,
Shankar Prasad Kanaujia
Research Student
C/O - Dr. K. Sekar
Bioinformatics Centre, SERC
Indian Institute of Science, Bangalore-12
Phone - 9480258032
Office - 080-2293-3059
On Sat, May 30, 2009 at 9:00 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Please keep all correspondence on the gmx-users list. I do not
advertise myself as a private tutor :)
Shankar Prasad Kanaujia wrote:
Dear Justin,
I have done simulation of protein-ligand complex using gromacs
v3.3.3.
The g_energy gives LJ-14, Coulomb-14, LJ-SR, Coulomb-SR energies,
however, it does not give LJ-LR and Coulomb-LR energy.
what could be the reason ?
It would be useful if you posted your .mdp file. Without it, I can
only guess why the LJ-LR term is missing. There is no such term
Coulomb-LR.
-Justin
thanking you.
--
Yours Sincerely,
Shankar Prasad Kanaujia
Research Student
C/O - Dr. K. Sekar
Bioinformatics Centre, SERC
Indian Institute of Science, Bangalore-12
Phone - 9480258032
Office - 080-2293-3059
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
