[gmx-users] stop mailing me
stop mailing me Marius Retegan <[EMAIL PROTECTED]> wrote: Hello I would like to know what charges are in the ffopls.rtp in the case of HISA. In the data below, on the 3rd column are the charges from Gromacs and on the 4th column are the charges for the same residue from a personal communication of opls parameters from prof. Jorgensen. [ HISA ] ; HISD in OPLS terminology [ atoms ] N opls_238 -0.500 -0.5000 H opls_241 0.300 0.3000 CA opls_224B 0.140 0.1400 HA opls_140 0.060 0.0600 CB opls_505 -0.297 -0.0050 HB1 opls_140 0.060 0.0600 HB2 opls_140 0.060 0.0600 CG opls_508 -0.261 0.0150 ND1 opls_503 -0.291 -0.5700 HD1 opls_504 0.326 0.4200 CD2 opls_507 0.504 -0.0150 HD2 opls_146 0.183 0.1150 CE1 opls_506 0.182 0.2950 HE1 opls_146 0.098 0.1150 NE2 opls_511 -0.564 -0.4900 C opls_235 0.500 0.5000 O opls_236 -0.500 -0.5000 Thank you Marius Retegan ___ gmx-users mailing list gmx-users@gromacs.org 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 - Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how.___ gmx-users mailing listgmx-users@gromacs.org 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
[gmx-users] stop mailing me
please stop mailing me, i am tired of all this mails
"Mu Yuguang (Dr)" <[EMAIL PROTECTED]> wrote:v\:*
{behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:*
{behavior:url(#default#VML);} .shape {behavior:url(#default#VML);}
st1\:*{behavior:url(#default#ieooui) }Dear Huey Ling,
In principle it is applicable. Then such REMD can be termed as Hamiltonian
REMD instead of canonical temperature REMD.
Dr. Yuguang Mu
School of Biological Sciences
60 Nanyang Drive
Nanyang Technological Uiversity
Singapre
Tel: +65-63162885
email:ygmuATntu.edu.sg
-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Huey Ling Tan
Sent: Tuesday, November 13, 2007 2:24 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] REMD As A Function of Distance Between 2 Chains
Hi all,
Is it feasible to do parallel tempering (replica exchange) as a function of
distance with umbrella sampling applied?
I can do REMD for a system containing 2 peptide chains as a function as
temperatures, where I grompp each of the systems at different temperatures, and
then gather the fullmd.tpr files in one folder with the script I want for full
md run.
But what if I want to do REMD as a function of distances (for example at 0.4,
0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file), at a fixed
temperature, with umbrella sampling applied? If this can be done, how should I
write the script for the full md run so that each of the pull.ppa files can
recognise the system that it suppose to pull?
If anyone know how this can be done?
Many thanks.
--
Best regards,
Huey Ling
___
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RE: [gmx-users] Tools for axial symmetry
stop mailing me please Berk Hess <[EMAIL PROTECTED]> wrote: Exactly the tools you mention do work: g_rdf has the option -xy trjorder does not assume anything about the geometry and will work fine in your case. Berk. >From: "Eudes Fileti" >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] Tools for axial symmetry >Date: Mon, 12 Nov 2007 10:59:54 -0200 > >Dear colleagues >I have made simulation of infinite nanotubes in solvent environment. >However I can not use the usual tools of the GROMACS to analyze my >simulation >(as g_rdf, trajorder, etc) due to axial symmetry (cylindrical). > >Problem that I need to solve are the calculation of rdf >(taking as reference the axis of the nanotube, not the COM) >and also the analysis of the number of molecules into the first solvation >shell. > >Have anybody some suggestion of standalone program or GROMACS tools for >help >me? > >Thanks >eef >-- >___ >Eudes Eterno Fileti >Centro de Ciência Naturais e Humanas >Universidade Federal do ABC >Rua Catequese, 242 - 3º Andar >09090-400 Santo André - SP Brasil >Tel: +55 11 4437-1600 ramal 408 >skype: eefileti >http://cromo.ufabc.edu.br/~fileti/ >___ >gmx-users mailing list gmx-users@gromacs.org >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 _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing list gmx-users@gromacs.org 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] How to set N-terminal lysine carry only +1 unit charge?
Hell my friend, i dont need any of this messages from all the members of this board, please help alert the board, its bored reading them all, i want to unsubscribe from the group Yang Ye <[EMAIL PROTECTED]> wrote: it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: > > Hi, > > > > I am using amber force field in Gromacs. The protein I simulated is > the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be > neutral. According to rules using Amber in Gromacs, neutral lysine > should be named to LYN. Everything goes smoothly except the N-terminal > lysine residue. It should carry +1 unit charge due to its location. > According to the rules, I should rename this residue as NLYN. But I > can not find NLYN in ffamber*.rtp. In other words, error will appear > if I do so. I did not get response from Dear Dr. Eric J. Sorin who > establish amber port into gromacs. So anyone knows how to set > N-terminal lysine residue carry +1, not +2 unit charges using Amber FF > in gmx? > > > > Zhongqiao > > > > National University of Singapore > > > > ___ > gmx-users mailing list gmx-users@gromacs.org > 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 ___ gmx-users mailing list gmx-users@gromacs.org 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org 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
