[gmx-users] MD with DNA double strand

Dear Gromacs users, I want to do a molecular dynamic simulation for my enzyme-ligand complex. The enzyme is topoisomerase I. I used the pdb id 1K4T for the simulation and I need to keep the DNA double strand with the enzyme. I replaced the 5'-sulfhydryl group into a 5'-hydroxyl group before

Re: [gmx-users] Fw:Re: on CHARMM-GUI produced lipid bilayer for gromacs use

Brett, Please do not mail me directly with such questions. I am not your tutor and I am not involved in the CHARMM-GUI. I forward this mail to the gromacs user list, as there may be someone who can and is willing to give suggestions there. But I do also like to note that the CHARMM-GUI is not

Re: [gmx-users] Choose index group from terminal input.

Hi, Yes. Further options at http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts Mark On Thu, Sep 17, 2015 at 1:04 PM Dawid das wrote: > O'right, I have figured that out myself. Just use text file like data.txt > with two lines: > 1 > 1 > > and

Re: [gmx-users] Electric double layer, how to add charge

Hello, thanks, very simple, changing the .top file worked perfectly. And I was thinking: How do I change the .gro file, will changing the .top be enough. thanks for the advice with the potential. I was thinking to calculate the potential (voltage) with the the poissons equation and the ion

[gmx-users] Choose index group from terminal input.

Dear Gromacs Experts, Let's say that for some reasons I don't want to specify the atom group when g_rms (or other module) prompts me to do so. So I do not want to see this: Select group for RMSD calculation Group 0 ( System) has 38387 elements Group 1 (Protein) has 3470

Re: [gmx-users] Choose index group from terminal input.

O'right, I have figured that out myself. Just use text file like data.txt with two lines: 1 1 and redirect it: g_rms [options] < data.txt 2015-09-17 11:32 GMT+01:00 Dawid das : > Dear Gromacs Experts, > > Let's say that for some reasons I don't want to specify the atom

[gmx-users] Problem with wall!

Dear all, I am a new gromacs user. I want to simulate a box with two charged walls contain water molecules, but i face to many problems! for example water molecules go out of box. Could anyone help me by explain details of wall simulation? Thanks in advance. Mahi -- Gromacs Users mailing list

Re: [gmx-users] GPU-accelerated desktop PC for MD simulations

Hi, The workstation hardware benchmarked in our recent paper [1] is quite decent. You should also browse the past discussions on the list. For best performance in a desktop setup a Haswell-E CPU (i7 4960X or 4930) and a GTX 980/980 Ti is the best bet, for something mid-range I'd go with a

Re: [gmx-users] GPU-accelerated desktop PC for MD simulations

On 9/16/15 9:18 PM, Gustavo Avelar Molina wrote: Hi everyone, I want to build a new GPU-accelerated desktop PC for MD simulations of relatively simple protein/carbohydrate systems. No QM-MM simulations is intended for now. For instance, I have been working with a protein of approximately 1500

Re: [gmx-users] Efficiently running multiple simulations

Hi Mark, Thank you for reviewing the log files! I will recompile GROMACS for AVX2_256 SIMD to efficiently use the CPUs. The number of cores on the node is 16 and each core has two threads. By default, GROMACS picked 4 threads per simulation. I reran the simulation by specifying 2 threads per

Re: [gmx-users] Atomic charges

Hello, from my own expierence I can say that atomic charges calculated with Gaussian are good charges. 2015-09-17 1:37 GMT-03:00 Pallavi Banerjee < pallavis...@students.iiserpune.ac.in>: > Thanks Justin. Things are clearer now. > > -Pallavi Banerjee > -- > Gromacs Users mailing list > > *

Re: [gmx-users] MD with DNA double strand

On 9/17/15 2:03 AM, Amali Guruge wrote: Dear Gromacs users, I want to do a molecular dynamic simulation for my enzyme-ligand complex. The enzyme is topoisomerase I. I used the pdb id 1K4T for the simulation and I need to keep the DNA double strand with the enzyme. I replaced the

[gmx-users] energygrps interactions are 0 for water

Hi, I have a problem regarding the calculation of interaction energies using gmx energy and the energygrps parameter in the mdp file. My mdp file includes the line energygrps = Ion OW Whenever I calculate the LJ-SR and Coul.-SR energy terms between OW and any other energy group, the result is

[gmx-users] GPU suggestions

Hello Gromacs users, We are running GROMACS molecular dynamics simulations on a cluster with the following specs: supermicro hardware, sandy bridge and haswell intel Xeons, 4 GB per core, Mellanox 10 GbE (w/RDMA) switching (no IB). We were thinking of adding GPU's to this system. Does anyone

Re: [gmx-users] Efficiently running multiple simulations

Hi, On Thu, Sep 17, 2015 at 6:24 PM Zimmerman, Maxwell wrote: > Hi Mark, > > Thank you for reviewing the log files! I will recompile GROMACS for > AVX2_256 SIMD to efficiently use the CPUs. > > The number of cores on the node is 16 and each core has two threads. By >

Re: [gmx-users] energygrps interactions are 0 for water

Hi, You're probably running on GPUs, and have missed the note in the .log file that observes that energy groups are not supported there (it'd be too slow to run). If you want such data, then the recommend procedure is to run your simulation normally, then use gmx mdrun -rerun old-trajectory -nb

Re: [gmx-users] New atom definition

On 9/17/15 3:08 PM, Maryam Kowsar wrote: Dear all, I want to use some atoms that are not implemented in gromacs. If i even make a .gro file, making a topology is a problem. What should i do? Derive parameters in a manner consistent with the desired force field and add all necessary bonded

[gmx-users] New atom definition

Dear all, I want to use some atoms that are not implemented in gromacs. If i even make a .gro file, making a topology is a problem. What should i do? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Choose index group from terminal input.

Thank you. 2015-09-17 12:37 GMT+01:00 Mark Abraham : > Hi, > > Yes. Further options at > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > > Mark > > On Thu, Sep 17, 2015 at 1:04 PM Dawid das wrote: > > > O'right, I have

Re: [gmx-users] Efficiently running multiple simulations

Hi, That doesn't make any sense unless someone else is on your node :-) Otherwise, maybe there's no pinning actually active? Try mpirun -np 8 mdrun_mpi -multi 8 -ntomp 1 -pin on -gpu_id 01234567 and look at the core usage. There should be 8 empty cores and no movement between them. Mark > > On

Re: [gmx-users] New atom definition

Thaks justin! I did it several times and it worked. But now when i want to add some neutral gas or heavy atoms it stops me with the error that the atom is not defined. I dont know where i make a mistake. On Friday, September 18, 2015, Justin Lemkul wrote: > > > On 9/17/15 3:08

[gmx-users] REMD and distance restraints problem in gmx 4.6.7

Dear Users: I have a system with many distance restraints, designed to maintain helical character, e.g.: [ distance_restraints ] 90 33 1 1 2 2.745541e-01 3.122595e-01 999 1.0 97 57 1 2 2 2.876300e-01 2.892921e-01 999 1.0 114 73 1 3 2 2.704403e-01 2.929642e-01 999 1.0 ... Distance restraints are