Re: [gmx-users] protein membrane simulation

)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 -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___

Re: [gmx-users] Restarting a crashed MD run

x-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:

[gmx-users] Implementation of time-dependent Electric Field

) trapezoidal pulse (1ns rise and fall times with 3ns pulse on time).Thanks in advance,-Viswanadham.-- Viswanadham Sridhara, Graduate Research Assistant,Old Dominion University,Norfolk, VA-23529. ___ gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Implementation of time-dependent Electric Field

Thanks for the quick feedback! On 5/10/06, Erik Lindahl <[EMAIL PROTECTED]> wrote: Hi,On May 10, 2006, at 1:24 PM, David van der Spoel wrote:> Viswanadham Sridhara wrote: >> Hi everyone,>> This is regarding implementation of time-dependent electric field>> on the system.

[gmx-users] PEO polymer

vance!-Vishy.-- Viswanadham Sridhara,Graduate Research Assistant,Old Dominion University,Norfolk, VA-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests t

Re: [gmx-users] PEO polymer

o simulate Poly Ethylene Oxide polymer in water?If so, are there any relevant websites and tutorials? I was involved in MD simulations of bilayers till now, and I know few sitesof Dr.Tieleman's etc. Similarly are there any for Polymers too?Thanks in advance!-Vishy.--Viswanadham Sridhara,Gradua

[gmx-users] pdb2gmx error

.-- Viswanadham Sridhara,Graduate Research Assistant,Old Dominion University,Norfolk, VA-23529. ___ 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

[gmx-users] E-zt ? (Time dependent electric field)

Hi everyone,I thought Time dependent Electric field  is fixed with Version 3.3.1.But the manual says it is not implemented and we can use only E-z instead of E-zt.Any ideas?Thanks,-Vishy -- Viswanadham Sridhara,Graduate Research Assistant,Old Dominion University,Norfolk, VA-23529

[gmx-users] Sodium Channel

Hi everyone,Did anyone do MD simulations on voltage gated sodium channel?I could find papers on MD simulations on KcsA potassium channels and stuff, but I could not find anywhere MD simulations on sodium channels. Thanks in advance,-Vishy-- Viswanadham Sridhara,Graduate Research Assistant,Old

[gmx-users] Gramicidin A

that I dont have to duplicate things.Thanks in advance-Vishy.Biophys J Vol 82, June 2002 pp. 2934-2924 by de Groot, Tieleman, Pohl, and Grubmuller. -- Viswanadham Sridhara,Graduate Research Assistant,Old Dominion University,Norfolk, VA-23529. ___ gmx

[gmx-users] Hen egg white lysozyme.

ut this.It is under HETATM section of .pdb file. Any help is appreciated.I know that I have to add this residue in aminoacids.dat file and create atoms and bonds in .rtp section. Is there any other way around? Thanks in advance,-Vissu-- Viswanadham Sridhara,Graduate Research Assistant,Old Dominion

Re: [gmx-users] Hen egg white lysozyme.

what it's used for (perhaps look up its name, andlook at the paper and PDB headers...). It is obviously harder to come up with parameters for NAG than not. Ifyou end up deciding it's not important, you can, for example, justremove the HETATM entries dealing with it before running pdb2gmx

Fwd: [gmx-users] Hen egg white lysozyme.

If you end up deciding it's not important, you can, for example, justremove the HETATM entries dealing with it before running pdb2gmx.DavidOn 8/7/06, Viswanadham Sridhara < [EMAIL PROTECTED]> wrote:> Hi Everyone,> I am trying to simulate a protein and I am getting the following

Re: Fwd: [gmx-users] Hen egg white lysozyme.

its name, and> look at the paper and PDB headers...).>> It is obviously harder to come up with parameters for NAG than not. If > you end up deciding it's not important, you can, for example, just> remove the HETATM entries dealing with it before running pdb2gmx.>> David>

Re: Fwd: [gmx-users] Hen egg white lysozyme.

= 0.3Thanks,-Vissu.On 8/11/06, David van der Spoel <[EMAIL PROTECTED]> wrote: Viswanadham Sridhara wrote:> Hello everyone,> I could figure out that parameters for NAG are not that important. So, I> used free HEWL.> I started running it, but I realize that the protein started to rotate &

[gmx-users] Free energy calculations

Hello gmx-users,I wanted to know whether there are any tutorials available on free energy calculations with Gromacs.I have done some survey, but was curious to find out any "decent" tutorials available. Thanks in advance,-Vissu.-- Viswanadham Sridhara,Research Assistant,Old Dominion

[gmx-users] cardiolipin / Cytochrome C

Hello gmx users,Were there any previous molecular dynamics simulations done on cardiolipin / Cytochrome C binding?Any "pdb" files available for either Cardiolipin or cytochrome C,. any literature available / any tutorials. Thanks in advance,-Vissu.-- Viswanadham Sridhara,Research Ass

Re: [gmx-users] GENION: Ions inside the protein

usersPlease 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 -- Viswanadham Sridhara,Research Assistant,Old Dominion Univers

Re: [gmx-users] plot rmsd of single atom / residue

iling_lists/users.php-- Viswanadham Sridhara, Research Assistant,Old Dominion University,Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests

Re: [gmx-users] plot rmsd of single atom / residue

   www interface or send it to [EMAIL PROTECTED] > [EMAIL PROTECTED]>.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> --> Viswanadham Sridhara,> Research Assistant,> Old Dominion University,> Norfolk, Va-23529.>>--

Re: [gmx-users] system net charge 0f -1.6

D].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Viswanadham Sridhara,Research Assistant,Old Dominion University,Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] Basic question.

as a very easy question for you guys, but I never looked into this earlier. Thanks in advance, -Vissu.-- Viswanadham Sridhara,Research Assistant,Old Dominion University,Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] question on energies

anual. Any suggestions? Thanks in advance, -Vishy-- Viswanadham Sridhara,Research Assistant,Old Dominion University,Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don&

Re: [gmx-users] What if the atom number exceed 99999 for Gromacs file?

org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Viswanadham Sridhara,Research Assistant,Old D

[gmx-users] Nucleic Acids -- Protonate ?

. This will be a lot of charge to neutralize by adding counter-ions, if I ignore hydrogens. Looking foward to your response. Best Regards, Vissu -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ gmx-users mailing

Re: [gmx-users] Nucleic Acids -- Protonate ?

ny Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: > Viswanadham Sridhara wrote: >> Hello, >> >> I wanted to perform MD simulation on a DNA struc

[gmx-users] Atoms in the .top ......

from, I checked .top, .gro files and they look fine, atleast to me. Looking forward to your response. Best Regards, Viswanadham -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ gmx-users mailing listgmx

Re: [gmx-users] Atoms in the .top ......

at you possibly did to it. Did you modify it? Cheers, Tsjerk On 2/13/07, Viswanadham Sridhara <[EMAIL PROTECTED]> wrote: > Hello all, > > when I run grompp, I am getting Fatal Error : Atoms in the .top are > not numbered consecutively. > > I checked the archives, this questi

[gmx-users] information on Na Channels in lipid bilayers ?

sodium permeability in Alamethicin and Gramicidin A. But, not much help with sodium channels. Looking forward to your response. Regards, Viswam. -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ gmx-users

Re: [gmx-users] Electric Field in part of the system

46 18 471 4205  fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED]    http://folding.bmc.uu.se___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or sen

Re: [gmx-users] internal vs external pressure

rg/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Viswanadham Sridhara,Graduate Research Assistant, Old Dominion U

[gmx-users] can not write a gro file without atom names

Hi everyone,I am trying to concatenate two .gro files obtained from two separate trajcetories.It says "can not write a gro file without atom names" with trjcat command.Any suggestions or any more info you required?? Thanks,-Viswam.-- Viswanadham Sridhara,Graduate Research Assistant,Ol

Re: [gmx-users] How can I ask a question??

ist    gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Viswanadham Sridhara,Graduate Research Assista

Re: [gmx-users] Not enough ref_t and tau_t values

st. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Viswanadham Sridhara,Graduate Research Assistant,Old Dominion University, "VIRGINIA". ___ gmx-users mailing list

Re: [gmx-users] problem with VMD

ilman/listinfo/gmx-usersPlease 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 -- Viswanadham Sridhara,Graduate Research Assistant,Old Dominion University,Norfolk, VA-23529. __

Re: [gmx-users] Re: Problem with simulated annealing!!!

MAIL PROTECTED].> Can't post? Read> http://www.gromacs.org/mailing_lists/users.php>__Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.o