[gmx-users] Doubt on membrane patch

Dear Gromacs users . I am working on membrane simulations, I have replicted the membrane patch of DPPC128.pdb using genconf with nbox. However almost 512 lipids seems larger for my GPCR and takes long computational time. How can I adjust the numbdr of lipids to become 300 patch, before inflation

[gmx-users] Regarding setting up the simulation box

Dear all, i am performing molecular dynamics for large complex with ~500,000 atoms. I have considered cubic box with 1nm distance from the molecule to the wall of the box. however this takes huge number of water molecules, hence i have manually visualized and edited the box inorder to reduce the

[gmx-users] gromacs installation

Hi, I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus. I am allotted to use only 2 nodes with 80 cpus. after installation when i did sample md run only 20 cpus are being utilized. How can I fully utilize the all 80 CPUs for mdrun. I have used below cmake command for the

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 161, Issue 20

; Today's Topics: > >1. Re: Incorrect link for release notes of gromacs 2016.3 > (Szil?rd P?ll) >2. Diffusion coefficient (Sohaib. Mohammed) >3. Re: Merging different topology files (Justin Lemkul) >4. Re: purpose of step pdb files during MD (Justin L

[gmx-users] Step.pdb generated during energy minimization

ns, simulation data seems fine. I did not find any other problems during equilibriation and production run. please suggest me if there is anything goes wrong? Best, Vijayakumar Gosu Ph.D Post Doctoral Fellow The Animal Genomics and Breeding Center Chonbuk National University Tel: +821073270

[gmx-users] How good to use triclinic box for gormacs simulations?

Hello all, I have performed simulations for Protein RNA complex around 1500 residues. I have used triclinic box with 1.4 nm distance from the edge of the box to protein as triclinic box takes less number of water molecules (~10) compared to other boxes . The simulation results looks fine and

[gmx-users] replicates with different random seed

... nvt.mdp ; Velocity generation gen_vel = yes gen_temp = 300 gen_seed = -1 Thanks in advance Best, Vijayakumar Gosu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http

[gmx-users] how can i restrain Zn ion during simulations

in advance Best, Vijayakumar Gosu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

[gmx-users] residue-ligand interaction energy using rerun option in mdrun

.. Thanks in advance. Vijayakumar Gosu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests v

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 71

Dear Justin, Thank you for your prompt response. I have one more query that can we use the modified trajectory for rerun option to recompute interaction energies with less number of frames, since i have long trajectory as well as large complex. Vijayakumar Gosu Ph.D On Thu, Aug 23, 2018

[gmx-users] Please provide some advice on my simulations

different compared to the second simulations despite same number of water molecules, box and parameters. Please provide some suggestions. Thanks a lot in advance. Best, Vijayakumar Gosu Ph.D Post Doctoral Fellow The Animal Genomics and Breeding Center Chonbuk National University Tel: +821073270537

[gmx-users] simulations being stopped during production run

= 2.0 ref_p = 1.0 compressibility = 4.5e-5 ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel = no *Thanks * *Vijayakumar gosu.* -- Gromacs Users mailing list * Please

[gmx-users] Regarding root mean square inner product from PCA

flag to extract the extreme conformation with 30 frames). I am bit confused to interpret the result. any suggestions please. Thanks in advance Vijayakumar Gosu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] multiple replica trajectory analysis

Dear Gromacs users, I have simulated a phosphorylated protein with 3 replicas (for 300ns). I concatenated the three replicas (total 900ns) for the analysis (1_2_3_trj_50ps.xtc). When I perform analysis the protein does not include the 3 phospho residues. However when I analyzed each replica