Re: [gmx-users] Is GPU GTX 560 compatible with GROMACS?

It is compatible with GROMACS. 在 2012年4月14日 上午11:32，Gaurav Goel 写道： > Dear All, > > Can you please guide me on how to find out if GeForce GTX 560 GPU card > by NVIDIA will be compatible with GROMACS? On the website GTX 560 Ti > is mentioned, but GTX 560 is not. > > Thanks, > G > > -- > Gaurav Goe

[gmx-users] Explicit solvent together with implicit solvent

Dear gromacs developers: I would like to simulate a reaction with 50 explicit water molecules with QM/MM (orca/gmx), and then add a implicit solvent model around this cluster (reaction center + 50 waters). But when I search the gromacs mailing list and gromacs manual, I get this “With the release

[gmx-users] Explicit solvent together with implicit solvent

Dear gromacs developers: I would like to simulate a reaction with 50 explicit water molecules with QM/MM (orca/gmx), and then add a implicit solvent model around this cluster (reaction center + 50 waters). But when I search the gromacs mailing list and gromacs manual, I get this “With the rele

[gmx-users] Explicit silvent together with implicit solvent model

Dear Gromacs developer: · I would like to simulate a reaction with 50 explicit water molecules with QM/MM (orca/gmx), and then add a implicit solvent model around this cluster (reaction center + 50 waters). But when I search the gromacs mailing list and gromacs manu

Re: [gmx-users] protein and DMPC in Charmm36 ff

Tomek Wlodarski wrote: Hi, I would like to simulate protein in DMPC bilayer in Charmm36 ff. I checked mailing list and KALP-15 tutorial, but still I have a few basic questions. 1) I have problem with DMPC bilayer... - VMD membrane builder only provides POPE and POPC lipids... - on the Pet

[gmx-users] protein and DMPC in Charmm36 ff

Hi, I would like to simulate protein in DMPC bilayer in Charmm36 ff. I checked mailing list and KALP-15 tutorial, but still I have a few basic questions. 1) I have problem with DMPC bilayer... - VMD membrane builder only provides POPE and POPC lipids... - on the Peter Tieleman page there is a p

Re: [gmx-users] Adding GROMOS force field to pdb2gmx

On 15/04/2012 9:54 PM, Marc Gordon wrote: Here is a brief summary of my situation: From what my copy of gromacs tells me pdb2gmx is using a 53a6 forcefield from 2004. I want to use the more recent carbohydrate specific 53a6_carbo force field. I have only managed to find this force field in GR

[gmx-users] Adding GROMOS force field to pdb2gmx

Here is a brief summary of my situation: >From what my copy of gromacs tells me pdb2gmx is using a 53a6 forcefield from 2004. I want to use the more recent carbohydrate specific 53a6_carbo force field. I have only managed to find this force field in GROMOS format. What I ultimately want is just t

[gmx-users] Clustering

Dear Erik, Thank you very much from your response, but I want to calculate the radius of these cluster. I want to know that I should do clustering with trjconv -cluster similar with micelle clustering and then calculate the radius of these? Best Regards Dina

[gmx-users] Using polarizable ff for ions in conjunction with free energy calculation

Hi all, I'm working on MD simluations including Free energy calculations of polarizable water and polarizable ions. Normal MD simulations for water and ions are working fine. But when starting Free Energy calculation for ions+water, the simulation immediately aborts, giving the error: /Progr

Re: [gmx-users] Clustering

Try g_clustsize Erik 15 apr 2012 kl. 09.00 skrev dina dusti: > Dear GROMACS Specialists, > > May I know about clustering, Please? > I want cluster small organic molecules. Is it possible? They collected in > some places together and they are separate in the other place. > Please help me. > >

[gmx-users] Clustering

Dear GROMACS Specialists, May I know about clustering, Please? I want cluster small organic molecules. Is it possible? They collected in some places together and they are separate in the other place. Please help me. Thank you very much in advance. Best Regards Dina-- gmx-users mailing listg