Re: [gmx-users] Problems during installation

Hi Szilard, Your advice was perfect: I've installed gromacs 2018_2 on my computer and I'm currently testing some sample runs which have speeded up 20 times! However, I consistently find that mdrun only selects one GPU when two are available. Why does this happen? *nvidia-smi* Fri Jul 20 12:22:26

[gmx-users] Setting correct non-bonded and pair (LJ) parameters in ffnonbonded.itp

Dear All, In my previous posts, I had written about errors arising upon changing the combination rule and using sigma and epsilon values. Dr Lemkul was kind enough to point out that incorrect formatting of the ffnonbonded.itp might cause errors and that the [nonbond params] as well as [pairtypes] s

Re: [gmx-users] Trouble running simulations with Nitrogen

Hi Try this http://erg.biophys.msu.ru/tpp/ Best On Thu, Jul 19, 2018 at 10:54 PM, Joshua Cummings < joshua.cummi...@uon.edu.au> wrote: > Hi Everyone, > > > I'm currently trying to run some simulations that involve the absorption > of N2 into a liquid solvent. I'm having some difficulty in gener

[gmx-users] Trouble running simulations with Nitrogen

Hi Everyone, I'm currently trying to run some simulations that involve the absorption of N2 into a liquid solvent. I'm having some difficulty in generating the topology for N2. For reference, the pdb file I have for N2 is as follows: HETATM1 N6B HDZ 0 0.000 0.000 0.553 1.0

[gmx-users] Calculate pore radius using water molecules

Dear GMX users, I would like to analyze a pore radius using the number of water molecules inside it. I do not have any experience. How can I count water molecules inside the pore? I want to get the time-dependent number of molecules inside the pore. Please advice me? Best regards, Miji -- Gro

[gmx-users] Compressing bundles of fibers into a surface

Dear gmx users I’m in the process of creating a PE polymer surface. pdb and itp files were obtained from ATB and were used to produce a (xyz) 142 x 6 x 60 A box ( starting size ) with 300 150 A long molecules. They were neatly aligned to start and - using pcoupletype = surface-tension

[gmx-users] surface tension in free energy calculation

Dear All, I’m simulating a system of monolayer/water interface and I want to calculate the change in the free energy (using Jarzynski method if possible) of my system in the following process. First, my system box is compressed to a certain size (by moving boundaries) and then it is expanded again

Re: [gmx-users] Problems during installation

On Mon, Jul 16, 2018 at 7:43 PM Rajat Desikan wrote: > Hi Mark, > > Thank you for the quick answer. My group is experimenting with a GPU-heavy > processor-light configuration similar to the Amber machines available from > Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our > un

Re: [gmx-users] CNT md simulation & unusual minimized structure

On 7/19/18 7:08 AM, Atila Petrosian wrote: Dear gromacs users, I am doing md simulation of cnt + drug (lig) + water molecules. I get lig.gro and lig.itp files using antechamber module and amb2gmx script. I used cnt force field parameters from paper (*https://pubs.acs.org/doi/abs/10.1021

Re: [gmx-users] energy minimization_note

On 7/19/18 6:18 AM, Atila Petrosian wrote: Dear Mark, Thanks for your answer. “But typically EM in vacuum is short enough you should not consider optimizing it.”. You are right. Using the reference manual about PME, I created new mdp file as follows: integrator = steep nst

[gmx-users] Ionic bonds

Hello, is there a difference in the implementation of an ionic bond and a covalent bond? For example UFF gives parameters for both atoms i and j. The atoms i and j should form an ionic bond and UFF gives me the parameters for the strecthing and bending potential. But in the case of dihedrals

[gmx-users] CNT md simulation & unusual minimized structure

Dear gromacs users, I am doing md simulation of cnt + drug (lig) + water molecules. I get lig.gro and lig.itp files using antechamber module and amb2gmx script. I used cnt force field parameters from paper (*https://pubs.acs.org/doi/abs/10.1021/jp011344u

[gmx-users] energy minimization_note

Dear Mark, Thanks for your answer. “But typically EM in vacuum is short enough you should not consider optimizing it.”. You are right. Using the reference manual about PME, I created new mdp file as follows: integrator = steep nsteps = 5 emtol