[gmx-users] Buffer Overflow Problem on Ubuntu Linux

ng this is appreciated. Venky ~ Venky Krishnamani Dr.Janos K. Lanyi Lab, D320, Medical Sciences I University of California, Irvine Irvine, CA 92697 ~ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

Re: [gmx-users] error in coordinate file

Carefully check the number of all the molecules listed in your topology file [ molecules ] section and verify if that corresponds exactly to the number of atoms in your coordinate file. You have added some extra atoms/molecules in the topology. Venky ~ Venky

Re: [gmx-users] A very Basic query

well I don't know if it can be done with gromacs... but sure can be using shell script + perl script. do something like this #!/usr/bin/perl while ($i<10) { system ("g_dist << EOF 13 14 EOF"); $i=$i+1; } Venky

Re: [gmx-users] No such moleculetype FE

On 4/30/07, Sonali <[EMAIL PROTECTED]> wrote: hi everybody, i am running Gromacs simulation with the protein 1f9b.pdb. I had earlier got some errors with the ligands present i.e FE, BCT and 3ID so i had run prodrg with BCT and 3ID but as prodrg server doesnot support for FE i had obtaine4d itp

Re: [gmx-users] Protein in SDS, GROMOS96 ff, MD crash - SDS molecule comes apart, LINCS error

Thanks again Tsjerk, I am making the required changes. Venky On Apr 25, 2007, at 1:06 PM, Tsjerk Wassenaar wrote: Hi Venky, Now I'm not sure whether putting the SDS and the solvent (SOL+Ions) together is the best idea. The temperature coupling groups have to do with the different beha

Re: [gmx-users] Protein in SDS, GROMOS96 ff, MD crash - SDS molecule comes apart, LINCS error

shouldn't cause any problems, but I just wanted to be sure. I am running the SDS simulations with water simultaneously... haven't checked its properties yet. Venky On 4/25/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Hi Venky, On 4/25/07, Venky Krishna <[EMAIL PROTECTED]> w

[gmx-users] Protein in SDS, GROMOS96 ff, MD crash - SDS molecule comes apart, LINCS error

0]={ 1.59138e+25, -2.53183e+25, 6.93924e+24} Inertia tensor[1]={-2.53183e+25, 4.38301e+25, -1.26821e+25} Inertia tensor[2]={ 6.93924e+24, -1.26821e+25, 8.36827e+24} $$ Regards, Venky. ___ gmx-users mailing listgmx-us

Re: [gmx-users] Energy Minimization problem

) and then energy minimize the system. Btw...did you define FLEXIBLE for water molecules during your em runs? Best Venky On Apr 18, 2007, at 5:24 PM, George Abadir wrote: Hi, I am doing an energy minimization for a carbon nanotube (end capped with hydrogen atoms) in a box of water. I

[gmx-users] Using ffgmx and ffG43a1 topologies

question is, can I use the GROMACS parameters of SDS molecules to directly derive its GROMOS96 params? If so how? P.S. If anybody has GROMOS96, SDS ff already, please help! You contribution will be much appreciated! Thanks Venky ___ gmx-users

[gmx-users] Mdrun Error

) --- What does it mean and how to go about correcting it? Thanks in advance. Venks -- Venky Krishnamani Graduate Student, Dr. Janos K. Lanyi Lab Univerisity of California, Irvine Irvine, CA (949) 202-9466 ___ gmx-users mailing listgmx-users

Re: [gmx-users] Problems Looking at Graphic Output

...from where you can download the dependencies (also in rpm) and finish install. Hope this helps Venks Venky Krishnamani Dr.Janos K. Lanyi Lab, D320, Medical Sciences D University of California, Irvine On Jun 1, 2006, at 11:54 AM, cesar wrote: Try installing VMD, this software is nice to

Re: [gmx-users] g_energy_d

as to make the selection unique.)I am not sure if you have a special option in the command line to display the numbersVenks Venky KrishnamaniDr.Janos K. Lanyi Lab,D320, Medical Sciences DUniversity of California, Irvine On May 31, 2006, at 5:21 PM, Arindam Ganguly wrote:Hi All,i am using the

Re: [gmx-users] POPC simulation

-That is all the modifications required for running the simulation. Hope this helps people with similar problem in the future.Venks Venky KrishnamaniDr.Janos K. Lanyi Lab,D320, Medical Sciences DUniversity of California, Irvine On May 29, 2006, at 12:23 PM,

Re: [gmx-users] Re: protein in popc

insertion into a bilayer.http://www.dddc.ac.cn/embo04/practicals/9_16.htmVenky Venky KrishnamaniDr.Janos K. Lanyi Lab,D320, Medical Sciences DUniversity of California, Irvine On May 15, 2006, at 5:13 AM, Shulin Zhuang wrote:I am very new to membrane modeling and hope to see more up-to-date proto

[gmx-users] Fatal Error: moleculetype K is redefined

ndif[ system ]; nameBR_POPC [ molecules ]; name    numberProtein 1POPC    56SOL 4412--- -- Venky KrishnamaniGraduate Student, Dr. Janos K. Lanyi LabUniverisity of California, Irvine Irvine, CA(949) 232-3021 ___ gmx-user