[gmx-users] membrane protein simulation - ligand introduction

Dear Users If membrane protein ligand complex needs to simulated in lipid bilayers then how to introduce ligand and at what step? regards -- B.Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

[gmx-users] GPU for free energy calculation?

Hello: I am going to calculate relative binding energy of ligands. I am just wondering can we use GPU for this task? I remembered that it is highly recommended to use double precision for free energy calculation considering accuracy, but current GPU version seems doesn't support double precis

[gmx-users] Conferences in 2014

Hello colleagues, I apologize if this list isn't the most appropriate place to such topic, but I'm looking for some good conferences/symposiums (etc) about Molecular Mechanics, structural biology, computational biology and related areas, and I'd like to know if someone has any suggestions. Is

[gmx-users] Embedded view of the users list

Hi, For the past several years and until a few weeks ago, the GMX-Users List webpage here ( http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List ) had an embedded "live"/"interactive" view of the list. Messages were organized in threads such that when I clicked on a thread, I could see all

Re: [gmx-users] GPU for free energy calculation?

Hi, The Verlet scheme supports free energy calculation in 5.0; it works with GPUs too, but not in double precision. However, I suggest you consider first whether you really *need* double precision. If you do, it may still be beneficial for you to use the Verlet scheme in 5.0 -- especially if you

Re: [gmx-users] Embedded view of the users list

On 5/10/14, 12:46 PM, Andrew DeYoung wrote: Hi, For the past several years and until a few weeks ago, the GMX-Users List webpage here ( http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List ) had an embedded "live"/"interactive" view of the list. Messages were organized in threads such

Re: [gmx-users] membrane protein simulation - ligand introduction

On 5/10/14, 4:23 AM, Balasubramanian Suriyanarayanan wrote: Dear Users If membrane protein ligand complex needs to simulated in lipid bilayers then how to introduce ligand and at what step? It's exactly like http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/ind

Re: [gmx-users] vdw radii in g_sas

Thank you Justin, Tsjerk and Antonio for your detailed answers. g_sas computes uses the truncation distance for residue contacts by considering the minimum distance between residues. However, the papers I referred to has a Calpha-Calpha or Cbeta-Cbeta cutoff of 10-12 angstrom (default g_sas trunca

[gmx-users] dssp installation error

dear gromacs users when i run do_dssp program 4.5 and 4.6 i saw below error plz help me progran do_dssp, version 4.5.3 source code file:do_dsso.c, line: 521 fatal error: failed to execute command: /usr/local/bin/dssp -na dd5iLsk0 ddj8721A > /dev/null2> /dev/null best regards elham tazikeh -- Gr

Re: [gmx-users] refcoord-scaling

Hi Mark We discussed this "refcoord scaling=com not working" quite a bit. With new version of gromacs 4.6.5, it seemed that com option is working fine. However, I later found out that it is only for equilibration run and system does blow up (domain decomposition error) in production run. Again to

Re: [gmx-users] GPU in Ubuntu

  Dear All,   I recently ran into a problem with a small geforce 610, and aside from woundering if it was worth the effort, found in Ubuntu 13.10 gromacs can not find the GPU.  The Nvidia site found this problem and states to install libcudart.5.5.so or higher, i tried this and the 6.0 as well,

Re: [gmx-users] GPU in Ubuntu

it is better to choose a stable Linux for computational work. I recommend the following: Redhat Enterprise, Scientific Linux,SuSE Linux Enterprise Ubuntu is on not stable enough for professional work according to my own experiences. On 05/10/2014 10:06 PM, lloyd riggs wrote: Dear All, I re

[gmx-users] poor minimization?

Hi I am simulating a system consisting of TiO2 crystal (2160 atoms position restrained), 3656 water molecules, 1 formate and 1 sodium ion. All of my energy minimizations (5000 steps or more) are getting over in few seconds (both for steepest descent as well as conjugate gradient). Would you call t

Re: [gmx-users] GPU in Ubuntu

Hi, First of all, the GeForce 610 is a rather basic card, in fact the most basic among the low-end ones. Unless the computer it is connected to is *very* slow (e.g. something like a dual-core CPU from 5+ years ago), my guess is that using it is not going to improve performance of a GROMACS simulat

Re: [gmx-users] GPU in Ubuntu

On Sat, May 10, 2014 at 10:40 PM, Albert wrote: > it is better to choose a stable Linux for computational work. I recommend > the following: > > Redhat Enterprise, Scientific Linux,SuSE Linux Enterprise > > Ubuntu is on not stable enough for professional work according to my own > experiences. Th

Re: [gmx-users] g_dipoles

I run g_dipoles for two ionic liquids : 1-Ethyl-3-methylimidazolium chloride and 1-Ethyl-3-methylimidazolium ethylsulfate. In both the systems cation is common 1-Ethyl-3-methylimidazolium. In g_dipoles comde static void neutralize_mols(int n,int *index,t_block *mols,t_atom *atom) { double mt

[gmx-users] water stretched apart

Dear All, I need help interpreting one image, that I am sharing via a link: https://www.dropbox.com/s/z1dly0jfhlftcmc/Screen%20Shot%202014-05-11%20at%2012.46.56%20AM.png It's a system of TiO2 crystal ( 2160 atoms, positions restrained with refcoord-scaling: com), 1 formate ion, 1 sodium ion and

Re: [gmx-users] water stretched apart

Hi Chetan, That's due to PBC. Use trjconv -pbc whole to fix it. Cheers, Tsjerk On May 11, 2014 8:12 AM, "Chetan Mahajan" wrote: > Dear All, > > I need help interpreting one image, that I am sharing via a link: > > > https://www.dropbox.com/s/z1dly0jfhlftcmc/Screen%20Shot%202014-05-11%20at%2012