Re: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

the archives? Best wishes, -Syma In message [EMAIL PROTECTED] minnale [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org writes: Thanks for your prompt reply, according to you for membrane protein protocols keep restrain only on protein but not on lipid and water

[gmx-users] lipid paraemeters

actually beginning to combine PT's lipid itps with ffG53a6 files. Many thanks in advance, -Syma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] running multiprocessor jobs on leopard 10.5.2

on a 2x quadcore (3.0 GHz) mac pros. Will post some benchmarks soon. Best wishes, -Syma *** Dr Syma Khalid RCUK Fellow (Chemical Biology) School of Chemistry University of Southampton Highfield

[gmx-users] memory requirements

-core for an 8 processor-core node).' by our HPC technicians. Any advice as to which I should go for, the 4 or 8 GB version? Any advice would be greatly appreciated. Best wishes, -Syma *** Dr Syma Khalid RCUK Fellow (Chemical

RE: [gmx-users] memory requirements

Hi Erik, Many thanks-it would be good to have the capabilities to simulate big systems so will go for 1GB per core. -Syma *** Dr Syma Khalid RCUK Fellow (Chemical Biology) School of Chemistry University

[gmx-users] langevin dynamics

counter ions (unfortunately my protein has an overall charge)? Obviously I would use periodic boundary conditions so the ions don't wander off. Many thanks in advance for your suggestions/comments, -Syma *** Dr

RE: [gmx-users] langevin dynamics

an overall neutral system. Is there some other way I can get a neutral system? Many thanks, -Syma *** Dr Syma Khalid RCUK Fellow (Chemical Biology) School of Chemistry University of Southampton Highfield

RE: [gmx-users] Self-assembly lipid simulation

Hi, The GROMACS user manual is a good place to start. For more specific help you will probably need to provide details of exactly what you want to do. What are you simulating? What are the questions you are hoping to answer? Best wishes, -Syma

RE: [gmx-users] lipid simulations

) trial and error. -Syma Dr. Syma Khalide-mail: [EMAIL PROTECTED] Dept. of Biochemistry phone: (0)1865-275380 University of Oxford fax: (0)1865-275273 South Parks Road

RE: [gmx-users] g_sdf again

Hi Thanks for your help with this. The problem was that the size of my 3d grid was too small (I was just using the default 1x1x1 nm). I have now used a grid size that matches my system and have a sensible gro file. Best wishes, -Syma _ From: [EMAIL PROTECTED] [mailto

[gmx-users] g_sdf again

is not positioned 'in' the box of density produced by g_sdf. Is this as it should be and I am interpreting my results incorrectly, or have I set up my coordinate system incorrectly? Many thanks in advance for help with this. -Syma *** Dr Syma Khalid

[gmx-users] help with g_sdf

as to how I would go about this? Many thanks, -Syma *** Dr Syma Khalid Department of Biochemistry, University of Oxford South Parks Road, Oxford OX1 3QU U.K

[gmx-users] g_rdf normalisation

should get three columns in the *.xvg output, the distance, the normalised data and the raw data, I only get two columns. Thanks in advance for any help. -Syma *** Dr Syma Khalid Department of Biochemistry

[gmx-users] langevin dynamics

wrong with the file I would appreciate your advice. Best wishes, -Syma *** Dr Syma Khalid Department of Biochemistry, University of Oxford South Parks Road, Oxford OX1 3QU U.K

[gmx-users] Langevin dynamics

Hi, I am still trying to do Langevin dynamics in gromacs- does anyone know (ball park) what would be reasonable values to use for the frictional term when simulating helical peptides in solution? Many thanks in advance, -Syma *** Dr Syma Khalid

[gmx-users] Langevin dynamics question

simulations, the frictional term should be scaled up too? Many thanks, -Syma *** Dr Syma Khalid Department of Biochemistry, University of Oxford South Parks Road, Oxford OX1 3QU U.K

[gmx-users] persistence length

Hi, I was just wondering if it is possible to calculate the persistence length of a long chain-like molecule with one of the gromacs analysis programs or if anyone has anything else that will do this? Thanks in advance, -Syma *** Dr Syma Khalid

[gmx-users] inter molecular distance restraints?

Hi, I was just wondering if is possible, in gromacs to apply distance restraints between molecules. So I have two ligands (part of the same complex) that I would like to keep together, even though they are not actually bonded together. Thanks in advance, -Syma