On 6/17/13 4:58 PM, Hyunjin Kim wrote:
Hi,
I sent the following email last Saturday and I haven't got any reply yet.
I wonder whether you can suggest something regarding this issue.
Thanks in advance.
**************************************************************************************
I edit my topology file for mutating CH --> COH during free energy
calculation.
Since one hydrogen atom attached to carbon disappears, while two O and H
atoms are appearing, I build topology file as follows:
8 opls_169 1 TEST O 3 -0.7 15.9994
opls_140 0.1 1.008
13 opls_140 1 TEST H6 4 0.1 1.008
opls_169 -0.7 15.9994
18 opls_155 1 TEST H10 5 0.455 1.008
DUM_155 0.0 1.008
25 DUM_155 1 TEST H15 7 0.000 1.008
opls_155 0.455 1.008
My questions are,
1. as you can see, I introduce a dummy atom in the A state and mutate H
--> O and dummy --> H. Is it correct?
Yes.
2. if it is correct, then how should I build bonded parameters between H
(opls_140) and dummy (opls_155), since they do not exist.
The interactions are simply zero.
I have searched for mailing list and tutorials, but I am still not clear
what is the correct way to edit topology file for my case.
There is a similar example in manual section 5.7.4 that may be useful.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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 gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
