Re: [gmx-users] Insertion of Ion-channels onto the membrane using g_membed with Amber force field

Thanks for the reply. For all-atom Amber ff, Should I change the neighbor list value or change in the cut-off for VdW interactions. As the side-chain hydrogen atoms might be clashing with the lipid atoms and thus producing many LINCS warning. Thanks Ram -- Gromacs Users mailing list * Please

Re: [gmx-users] Insertion of Ion-channels onto the membrane using g_membed with Amber force field

Hi, What's the question? :-) Sounds like maybe you need to be more gentle when using all-atom Amber models than GROMOS ones that may not be? Mark On Wed, Dec 6, 2017, 5:30 PM Dhaniram Mahato wrote: > Hi there, > > g_membed is not able to fix the clashes while using the

[gmx-users] Insertion of Ion-channels onto the membrane using g_membed with Amber force field

Hi there, g_membed is not able to fix the clashes while using the Amber force field, but when I use the gromos force field , it can fix the clashes and also It can insert the big protein onto the membrane perfectly. Thanks Ram -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Using custom potential for electrostatics between protein and water

Hi, User tables for nonbonded interactions, including pme-user are only supported with the group cutoff scheme, not verlet. grompp should give a fatal error to tell you that, sorry. Mark On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan wrote: > Hello, > > I am trying to

Re: [gmx-users] Metal-Protein interactions

On 12/5/17 2:10 PM, RAHUL SURESH wrote: On Tue, 5 Dec 2017 at 6:02 PM, Justin Lemkul wrote: On 12/5/17 4:16 AM, RAHUL SURESH wrote: Dear Justin The topology says the Copper ion is with +2 charge. Thank you Here for the command *"gmx grompp -f em.mdp -c solv.gro -p

[gmx-users] Using custom potential for electrostatics between protein and water

Hello, I am trying to use a custom electrostatic potential between protein and water, with protein-protein and water-water potentials remaining the same. I tried running the simulation with the following input script: define = -DPOSRES ; position restrain for protein

Re: [gmx-users] How the index is recognised for values more than 99999?

Hi, The numbering of the coordinate file is not significant for this, precisely for that reason. Mark On Wed, Dec 6, 2017, 7:20 AM ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs,I am doing the RMSD calculation for a particular group of > protein residues. My system also has water

[gmx-users] How the index is recognised for values more than 99999?

Dear Gromacs,I am doing the RMSD calculation for a particular group of protein residues. My system also has water molecules so there are more than 9 atoms. Thus, the 10th atom is indexed as 0, and 11th atom as 1, and so on. So if the index file for my group has an entry of 1, how

Re: [gmx-users] Fwd: lost particles while sorting

Hi, If you think the software has a bug please open an issue at https://redmine.gromacs.org and attach a full description and tpr. Multiple people have observed this but the developers have not and can't fix it until they have a way to reproduce it, please :-) Mark On Wed, Dec 6, 2017, 5:58 AM

Re: [gmx-users] Metal-Protein interactions

On Tue, 5 Dec 2017 at 6:02 PM, Justin Lemkul wrote: > > > On 12/5/17 4:16 AM, RAHUL SURESH wrote: > > Dear Justin > > > > The topology says the Copper ion is with +2 charge. > > Thank you > > > > Here for the command *"gmx grompp -f em.mdp -c solv.gro -p cu.top -o > > ions.tpr"

[gmx-users] Fwd: lost particles while sorting

​​Hi, Sorry for reposting my query. I don't see a way to fix this software inconsistency issue. I am running NPT equilibration on gpu. After I finished the NVT I got an error saying Software Inconsistency Error: Lost particles while sorting (6 out of 8) Now I looked into the archive and it

Re: [gmx-users] DSSP

There's no DSSP version 3 that I know of. That can't be right. J On Tue, Dec 5, 2017 at 5:52 PM, Vidya R wrote: > Hi, > > I have installed dssp version > > > *3.0.0-win32* > > *What should be the command now?* > > On Tue, Dec 5, 2017 at 10:08 PM, João Henriques < >

Re: [gmx-users] DSSP

Hi, Please follow the instructions at gmx do_dssp -h Mark On Wed, Dec 6, 2017, 3:52 AM Vidya R wrote: > Hi, > > I have installed dssp version > > > *3.0.0-win32* > > *What should be the command now?* > > On Tue, Dec 5, 2017 at 10:08 PM, João Henriques < >

Re: [gmx-users] Help to interpret the energy terms for gmx energy

Hi, On Wed, Dec 6, 2017, 3:11 AM Jose wrote: > Hi all, > > My simulated system is a lipid bilayer of lipid+cholesterol simulated > with coulombtype=PME. I have calculated the energy terms corresponding > to Coul-SR and LJ-SR as a measure of the electrostatic and van der Waals >

Re: [gmx-users] Pressure through one direction

Hi, Yes, anisotropic coupling is described there. Mark On Wed, Dec 6, 2017, 3:53 AM ali akgün wrote: > I mean can i run npt only one direction? > > On Tue, Nov 28, 2017 at 10:53 PM, Wes Barnett > wrote: > > > On Tue, Nov 28, 2017 at 12:25 PM,

Re: [gmx-users] DSSP

Hi, I have installed dssp version *3.0.0-win32* *What should be the command now?* On Tue, Dec 5, 2017 at 10:08 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Did you specify the DSSP version as the error message suggests? DSSP > version 2 has different syntax from the previous

Re: [gmx-users] DSSP

Did you specify the DSSP version as the error message suggests? DSSP version 2 has different syntax from the previous one. On the gromacs 5.1.4 do_dssp assumes that you're using version 2, but maybe yours is version 1. P.S.: I am assuming you have done everything else correctly, i.e., you have a

[gmx-users] Help to interpret the energy terms for gmx energy

Hi all, My simulated system is a lipid bilayer of lipid+cholesterol simulated with coulombtype=PME. I have calculated the energy terms corresponding to Coul-SR and LJ-SR as a measure of the electrostatic and van der Waals interactions. However after reading some literature and posts I have a

[gmx-users] trjcat options

Hi, I am trying to concatenate two consecutive md trajectories. Each of them were run for 100 ns. e.g. traj-1: 0-100 ns, traj-2: 0-100 ns (but started from the final structure of traj-1). So, basically I want to prepare a final trajectory of 0-200 ns. So , I am using the following command:

[gmx-users] request

whats causes this error? Command line: gmx mdrun -s md_0_1 -cpi md_0_1.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1.cpt are not present or not named as the output files by the current program: Expect output files present: Expected

Re: [gmx-users] DSSP

I got the error dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2> /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1# --- Program gmx do_dssp, VERSION 5.1.4 Source code file:

[gmx-users] Tutorial for calculating diffusion from umbrella sampling

Dear Experts,Is there any tutorial available online for understanding procedure to calculate diffusion coefficient from umbrella sampled force and position trajectory data. The formula for diffusion is given as D()=variance(z)/tau. Numerator is variance of z (or

Re: [gmx-users] DSSP

Hi! This is not so much for you as it is for the other users and developers. I think I found a problem with the DSSP code when compiling using the latest boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the "include" directory of this new boost, and the compilation fails. The error

Re: [gmx-users] Metal-Protein interactions

On 12/5/17 4:16 AM, RAHUL SURESH wrote: Dear Justin The topology says the Copper ion is with +2 charge. Thank you Here for the command *"gmx grompp -f em.mdp -c solv.gro -p cu.top -o ions.tpr" *I get two notes. Note one descripbe the non-zero charge of the system and note 2 states as,

Re: [gmx-users] Topology file of molecule

Dear Vytautas and Justin, Thank you both for the help. I will try to perform some dihedral scans of small and simple molecules. Best regards, Krzysztof 2017-12-04 15:24 GMT+01:00 Justin Lemkul : > > > On 12/4/17 5:31 AM, Krzysztof Kolman wrote: > >> Dear Justin, >> >> Since

Re: [gmx-users] Metal-Protein interactions

Dear Justin The topology says the Copper ion is with +2 charge. Thank you Here for the command *"gmx grompp -f em.mdp -c solv.gro -p cu.top -o ions.tpr" *I get two notes. Note one descripbe the non-zero charge of the system and note 2 states as, *Removing all charge groups because