Re: [gmx-users] Optimal Hardware for Gromacs

Hi, Actualy suppermicro offers 4 socket machines with 12-core amd cpus so you get 48cores in 1U GROMACS perform well on such hardware =) In case of using Infiniband you need IB switch of dual port ib cards (to connect machines as a 1d torus) 2010/4/28 David van der Spoel > On 4/28/10 9:38 AM,

Re: [gmx-users] Optimal Hardware for Gromacs

On 2010-05-02 10.32, Alexey Shvetsov wrote: Hi, Actualy suppermicro offers 4 socket machines with 12-core amd cpus so you get 48cores in 1U GROMACS perform well on such hardware =) Sure but a simple rule of thumb is that you want to maximize aggregate clockspeed per dollar. Such machines migh

Re: [gmx-users] g_wham gets stuck

Thank you Jochem, In your last reply, did you mean that i can perform the WHAM on Various histograms that were collected with different force constants? i mean , will it know to do the correction for the biasing potential amir On Fri, Apr 30, 2010 at 4:00 PM, Jochen Hub wrote: > Justin A. Lemkul

[gmx-users] amber 03 forcefield

Hi gromacs users I will use amber 03 forcefield for simulation of protein-dna interaction. but why ffamber03.atp is as follow : amber99_0 1.00800 ; H0 H aliph. bond. to C with 1 electrwd. group (03GLY) amber99_1 79.9 ; BR bromine amber99_2 12.01000 ; C sp2 C carbo

Re: [gmx-users] amber 03 forcefield

shahab shariati wrote: Hi gromacs users I will use amber 03 forcefield for simulation of protein-dna interaction. but why ffamber03.atp is as follow : amber99_0 1.00800 ; H0 H aliph. bond. to C with 1 electrwd. group (03GLY) amber99_1 79.9 ; BR bromine amber99_2

[gmx-users] DNA strands disconneting from each other along MD simulations

Hi GROMACS users ! I am using amber force field to perform 10 ns MD simulations of a DNA dodecamer docked with small molecules in order to check if these molecules stay between the strands interacting with the nucleotides, but, after the simulations, I've observed that sometimes the DNA s

Re: [gmx-users] DNA strands disconneting from each other along MD simulations

Tanos C. C. Franca wrote: Hi GROMACS users ! I am using amber force field to perform 10 ns MD simulations of a DNA dodecamer docked with small molecules in order to check if these molecules stay between the strands interacting with the nucleotides, but, after the simulations, I've obse

Re: [gmx-users] Optimal Hardware for Gromacs

2010/5/2 David van der Spoel > On 2010-05-02 10.32, Alexey Shvetsov wrote: > >> Hi, >> >> Actualy suppermicro offers 4 socket machines with 12-core amd cpus so >> you get 48cores in 1U >> GROMACS perform well on such hardware =) >> > > Sure but a simple rule of thumb is that you want to maximize

Re: [gmx-users] Reg: Running gromacs on a condor cluster

On 30.04.2010, at 16:04, Esztermann, Ansgar wrote: > On Apr 30, 2010, at 14:46 , Rohit Farmer wrote: >> >> Hi everyone.. >> >> I just made a small two node condor cluster and was trying to run gromacs on >> it ... so i used the vanilla environment and placed the gromacs mdrun >> command in a

[gmx-users] how to show structure results in Martini coarse-grained simulation?

Dear user: how to show struture or conformation in Martini coarse-grained simulation, using VMD or other? Please give me some suggestion! thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] simple question about rtp and pdb file

Dear Justin, Thank you so much for your help. Could you please help me with some simple questions: 1- Regarding the atom types: For n-Hexane why did not you choose atom types: opls_068 15.03500 ; CH3 (C2) N-ALKANES opls_071 14.02700 ; CH2 (SP3) ALKANES rather than: opls_157 12.01100

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

xi zhao wrote: Dear user: how to show struture or conformation in Martini coarse-grained simulation, using VMD or other? Please give me some suggestion! thank you! What kind of rendering do you want to do? There are some scripts linked below to render bonds in a CG structure. http://www

Re: [gmx-users] simple question about rtp and pdb file

Moeed wrote: Dear Justin, Thank you so much for your help. Could you please help me with some simple questions: 1- Regarding the atom types: For n-Hexane why did not you choose atom types: opls_068 15.03500 ; CH3 (C2) N-ALKANES opls_071 14.02700 ; CH2 (SP3) ALKANES rather than: op

[gmx-users] Help for running gromacs

I am using Gromacs for Simulation of Insulin.I have generated most of the files but unable to generate the ions.pdb file.The system is becoming idle after the Selection command. A line on the command prompt appears as "replacing solvent molecule with Na" and remains as such for many hours. Is this