[gmx-users] shake and settle
Hi gmx user I want to use shake algorithm for bonds within protein and settle algorithm for the bonds of the water. How do I specify two different constraints algorithm in pr.mdp file? Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shake and settle
- Original Message - From: subarna thakur thakur.suba...@yahoo.co.in Date: Saturday, May 22, 2010 19:23 Subject: [gmx-users] shake and settle To: gmx-users@gromacs.org --- | Hi gmx user I want to use shake algorithm for bonds within protein and settle algorithm for the bonds of the water. How do I specify two different constraints algorithm in pr.mdp file? Subarna Thakur [ settles ] in your water .itp file chooses settle. You can choose LINCS or SHAKE in the .mdp file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] shake vs settle for water
Hi All, I am using Groamcs 3.2.1 for my simulations, I am having some problems with an interfacial system when I use SETTLE as opposed to SHAKE to constrain OH bonds and HOH angle in water. As a matter of fact I did various simulations of liquid vapor interface simulations of water, SETTLE gives me absurd numbers while SHAKE gives consistently good results . I have looked up the mailing list as well as manual for differences in SHAKE and SETTLE, but apart from the statement that SETTLE Is better than SHAKE I dint find much. Any ideas on how to resolve this. When I look at OH bond and HOH angle distribution from SETTLE and SHAKE its precisely same. Any insights would be helpful, Thanks Rahul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] shake vs settle for water
Rahul Godawat wrote: Hi All, I am using Groamcs 3.2.1 for my simulations, I am having some problems with an interfacial system when I use SETTLE as opposed to SHAKE to constrain OH bonds and HOH angle in water. As a matter of fact I did various simulations of liquid vapor interface simulations of water, SETTLE gives me absurd numbers while SHAKE gives consistently good results . I have looked up the mailing list as well as manual for differences in SHAKE and SETTLE, but apart from the statement that SETTLE Is better than SHAKE I dint find much. Any ideas on how to resolve this. When I look at OH bond and HOH angle distribution from SETTLE and SHAKE it’s precisely same. more details please. time step, cutoffs, PME OS why 3.2.1? Any insights would be helpful, Thanks Rahul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
