[gmx-users] pressure is coming 1.39

Hi,, I am doing a simulation of peptide in water. After 10 ns npt equilibration the average pressure is coming 1.39 and density is coming 1005.71 kg/m3. Can I proceed for production run? And what is the upper and lower limit for the pressure ...after which we can continue production run? --

[gmx-users] gromacs lincs warning: relative constraint deviation after lincs

Hi, I am trying to run multiple (1000) md simulations using a shell script. Some of the simulations (say simulation no. 56) shows error " lincs warning: relative constraint deviation after lincs" and get paused there. In that case, i have to manually abort that particular simulation (using

Re: [gmx-users] Application of External Forces on Lipid Membrane

Would the application of surface tension work for you ? > On 6,Sep 2019, at 5:45 PM, Shivam Suthendran wrote: > > Hi there, > > I just completed the tutorial for KALP in DPPC membrane. I'm wondering > how I would go about the application forces on the lipid membrane. Any and > all input would

[gmx-users] The problem of utilizing multiple GPU

Hello Szilárd Páll Thank you for you reply. I tried your command: gmx mdrun -ntmpi 7 -npme 1 -nb gpu -pme gpu -bonded gpu -gpuid 0,2,4,6 -gputask 001122334 but got the following error information: Using 7 MPI threads Using 10 OpenMP threads per tMPI thread Program: gmx mdrun,

Re: [gmx-users] The problem of utilizing multiple GPU

Hello Szilárd Páll Thank you for you reply. I tried your command: gmx mdrun -ntmpi 7 -npme 1 -nb gpu -pme gpu -bonded gpu -gpuid 0,2,4,6 -gputask 001122334 but got the following error information: Using 7 MPI threads Using 10 OpenMP threads per tMPI thread Program: gmx mdrun, version

Re: [gmx-users] Application of External Forces on Lipid Membrane

Hi there, I just completed the tutorial for KALP in DPPC membrane. I'm wondering how I would go about the application forces on the lipid membrane. Any and all input would be greatly appreciated. Thank you -- Shivam Suthendran "Diamonds are forever. E-mail come close" -- Gromacs Users

Re: [gmx-users] Ionization with different ions of different concentrations

On 9/6/19 12:45 PM, Mohammed I Sorour wrote: Dear Gromacs users, I'm trying to add MgCl2 (100 mM) and NaCl (6 mM) to my system which has (-22 net charge). I add a neutralizing amount of Mg or Na using the genion neutral option. But when it comes to the salt concentration, I'm failing to

Re: [gmx-users] Molecule contains no atoms

On 9/6/19 11:13 AM, Tanos Franca wrote: Dear users, GROMACS 5.1.4 is returning the error message below after running grompp with stpr.mdp. Does anyone knows how to fix it? Program gmx grompp, VERSION 5.1.4 Source code file:

[gmx-users] Ionization with different ions of different concentrations

Dear Gromacs users, I'm trying to add MgCl2 (100 mM) and NaCl (6 mM) to my system which has (-22 net charge). I add a neutralizing amount of Mg or Na using the genion neutral option. But when it comes to the salt concentration, I'm failing to have both of the salts added simultaneously. Like

Re: [gmx-users] simulation on 2 gpus

On Fri, Sep 6, 2019 at 3:47 PM Stefano Guglielmo wrote: > > Hi Szilard, > > thanks for suggestions. > > > As for the strange crash, the workstation works fine using only cpu; the > problem seems to be related to gpu usage, when both cards are used for 200 > W over 250 (more or less) the

Re: [gmx-users] Fatal error: Atom O4 in residue GLU 7 was not found in rtp entry

Yeah! But I don't want any charge at terminal residues. I think I should cap these by acetyl or amide moiety. Let me try this. On Fri, 6 Sep 2019, 19:45 Justin Lemkul, wrote: > > > On 9/6/19 4:32 AM, Navneet Kumar Singh wrote: > > Hello Everyone! > > > > I am trying to simulate five peptides

[gmx-users] Fat-bottom restrain

Dear all, Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have a smaller cubic box as semi-preamble walls inside a bigger cubic box so that all molecules except water would stay inside the smaller box during the simulation, however, the wall doesn't work and the molecules are

[gmx-users] Non-bonded interactions settings using Amber

Dear All, I am using amber99fb-star-ildn with Gromacs2016.3 and I'm not sure how to choose some options for non-bonded interactions such as vdw-modifier (potential-shift or potential-shift-verlet or potential-switch) dispcorr (EnerPres or no) rcoulomb rvdw I read original papers about

[gmx-users] Molecule contains no atoms

Dear users, GROMACS 5.1.4 is returning the error message below after running grompp with stpr.mdp. Does anyone knows how to fix it? Program gmx grompp, VERSION 5.1.4 Source code file: /home/cuda1/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c, line: 1001 Fatal error: Molecule type

Re: [gmx-users] Fatal error: Atom O4 in residue GLU 7 was not found in rtp entry

On 9/6/19 4:32 AM, Navneet Kumar Singh wrote: Hello Everyone! I am trying to simulate five peptides along with water using GROMACS. I have used the PACKMOL to prepare initail PDB files. Peptide were made using Schrodinger Maestro. I have got a final PDB file having the water molecules and

Re: [gmx-users] Forcefield parameter for transition metal

On 9/5/19 3:07 AM, Srijan Chatterjee wrote: Hi Justin, "The force fields in GROMACS are (by design) biomolecular in nature. None support tungsten." Thanks for clarifying. I happen to just come across a paper with similar forcefield values (https://doi.org/10.1016/j.jct.2019.01.016) Although

Re: [gmx-users] simulation on 2 gpus

Hi Szilard, thanks for suggestions. As for the strange crash, the workstation works fine using only cpu; the problem seems to be related to gpu usage, when both cards are used for 200 W over 250 (more or less) the workstation turns off. It is not about PSU (even in the "offending" case we are

[gmx-users] Fatal error: Atom O4 in residue GLU 7 was not found in rtp entry

Hello Everyone! I am trying to simulate five peptides along with water using GROMACS. I have used the PACKMOL to prepare initail PDB files. Peptide were made using Schrodinger Maestro. I have got a final PDB file having the water molecules and randowmly distributed peptides. After that I am