Re: [gmx-users] pulling direction in Umbrella sampling

2013-04-14 Thread Justin Lemkul 



On 4/14/13 2:09 AM, Kshatresh Dutta Dubey wrote:

Dear Users,

I am using umbrella sampling method for unwinding of a peptide from binding 
site. I have to pull peptide in -X (negative direction). Can anyone suggest me 
keyword for this purpose. Should I use pulling_dim = Y N N or have to define 
some other keywords.



Set pull_rate1 < 0 or otherwise use a different pull_geometry that allows you to 
specify pull_vec1, which allows you to set positive and negative vectors.


-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 listgmx-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

[gmx-users] pulling direction in Umbrella sampling

2013-04-13 Thread Kshatresh Dutta Dubey 
Dear Users,

I am using umbrella sampling method for unwinding of a peptide from binding 
site. I have to pull peptide in -X (negative direction). Can anyone suggest me 
keyword for this purpose. Should I use pulling_dim = Y N N or have to define 
some other keywords.

I will be thankful for every help. Thanking you in advance.

Regards 
Kshatresh Dutta Dubey

--
gmx-users mailing listgmx-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