Re: [gmx-users] Group NS scheme parameter for 2016.3 version

> -Original Messages- > From: "Mark Abraham" > Sent Time: 2017-09-26 06:38:40 (Tuesday) > To: "Discussion list for GROMACS users" , "Discussion > list for GROMACS users" > Cc: > Subject: Re:

Re: [gmx-users] Regarding setting up the simulation box

Hi, And choose your cell shape wisely. Biology need not be cubic ;-) Mark On Tue, 26 Sep 2017 02:27 Dallas Warren wrote: > There is no "wall". > > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > >

Re: [gmx-users] Regarding setting up the simulation box

There is no "wall". http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions https://twitter.com/dr_dbw/status/909559339366572032 What is important is the distance with itself, through the PBC. The complex should not interact with itself. Catch ya, Dr. Dallas Warren Drug

Re: [gmx-users] Necessary files to restart/continue REMD

Hi, Details vary with the version of GROMACS and exactly how you ran initially. Multidir option is more reliable than multi option. Obviously you always need the checkpoint and tpr files. Otherwise, to append you need everything the same, and to use noappend there are no further requirements.

Re: [gmx-users] restrained md_coordinate issue

Hi, Restraints don't freeze the coordinates, you must expect movement. Mark On Fri, 22 Sep 2017 13:49 wrote: > Hello Everyone > > I have simulated a protein - ligand complex with gromacs 5.1.4 for 100ns. > > I have restrained the position of the ligand ( which in my case

Re: [gmx-users] How to correctly setup gmx_mpi mdrun

Hi, You need a correctly set up MPI environment. My experience of linux distro packages has been excellent, so pick one and consult its documentation. Mark On Fri, 22 Sep 2017 23:46 Zheng Ruan wrote: > Hi Gromacs Users, > > I'm learning how to run a simple replica

Re: [gmx-users] Fwd: Calculating nonbonded energy

Hi, There's no free lunch. If you want to calculate an energy then you need a model physics - ie a topology. But even when you do, the distinction of being part of the nonbonded interactions is physically meaningless, so I would reconsider your approach. Mark On Sat, 23 Sep 2017 14:44 Mohan

Re: [gmx-users] Group NS scheme parameter for 2016.3 version

Hi, On Mon, 25 Sep 2017 14:11 Du, Yu wrote: > Dear GMX Users, > > > Indeed making tabulized potential between groups with Verlet is not > trivial as also discussed in OpenMM issue #1765. > > I'm using gmx 2016.3. If I want use the group NS scheme as precise as > possible, what

Re: [gmx-users] wall time for every 1000 steps in simulation - reg

Hi, I'm not sure what you mean by wall time or actual time, but the answer is no :-) Mark On Mon, 25 Sep 2017 12:10 Meagha ramana kumar wrote: > Hi, > > > Is it possible to get actual wall time (0 to total time) every 1000 steps, > instead of expected time? > > thanks >

Re: [gmx-users] compilation of gromacs 2016.3 or 4 with C compiler flag -fdebug-prefix-map=/build/gromacs-GTZ9iZ/gromacs-2016.1=.

Hi, Clearly you have multiple versions installed and your dynamic linking setup is confused. Please follow the instructions for doing this reliably, found in the installation instructions at

Re: [gmx-users] Simulation in NPgT ensemble

Thanks, Andre! but I have found a lot of peppers, where people have applied constant surface tension simulation using Semi-isotropic coupling. Assuming that the stretching of the membrane is produced via difference in the ref_p along z and xy directions, does the pcoupltype=surface-tension

Re: [gmx-users] Simulation in NPgT ensemble

it is quite well explained in the manual, pcoupltype=surface-tension Andre On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 wrote: > Dear Gromacs users! > > I wonder to ask whether is possible to perform simulations in NPgT ensemble > with the explicit definition of the

Re: [gmx-users] New files after simulation run

> Hi All, > > I have run an extended simulation for 90ns like this: (my previous run was > for 10ns) > > grompp -f new.mdp -c old.tpr -o new.tpr > mdrun -s new.tpr -cpi old.cpt > > I output mdrun STDOUT to an output file and it looks like this: > > ## >

[gmx-users] compilation of gromacs 2016.3 or 4 with C compiler flag -fdebug-prefix-map=/build/gromacs-GTZ9iZ/gromacs-2016.1=.

Thank you James for your quick reply ! I indeed call the executable obtained by compiling the gromacs2016.3 files. Calling with the explicit path give me the same results (see below) Since, as you, I first suspected that I had some mixing between path definitions, I reinstalled

Re: [gmx-users] compilation of gromacs 2016.3 or 4 with C compiler flag -fdebug-prefix-map=/build/gromacs-GTZ9iZ/gromacs-2016.1=.

On Mon, Sep 25, 2017 at 7:44 AM, Claire Loison wrote: > > Dear gmx users, > > I am trying to compile gromacs 2016.3 (or 2016.4) on a linux > workstation (Linux ilmfixe160 4.7.0-1-amd64 #1 SMP Debian 4.7.5-1 > (2016-09-26) x86_64 GNU/Linux). > > The compilation seems

[gmx-users] compilation of gromacs 2016.3 or 4 with C compiler flag -fdebug-prefix-map=/build/gromacs-GTZ9iZ/gromacs-2016.1=.

Dear gmx users, I am trying to compile gromacs 2016.3 (or 2016.4) on a linux workstation (Linux ilmfixe160 4.7.0-1-amd64 #1 SMP Debian 4.7.5-1 (2016-09-26) x86_64 GNU/Linux). The compilation seems to work smoothly and in fact tests simulations (EM, MD, ... ) are even performed almost as

[gmx-users] Group NS scheme parameter for 2016.3 version

Dear GMX Users, Indeed making tabulized potential between groups with Verlet is not trivial as also discussed in OpenMM issue #1765. I'm using gmx 2016.3. If I want use the group NS scheme as precise as possible, what parameters in mdp file should I set and what are their recommended

[gmx-users] distance/bonds restrains in gromacs2016.3 with domain decomposition

Dear all, I try to restrain the conformation of a protein using distance/bonds restrains. I have a problem when I try to use distance restraints or restraint potential (bonds type 10) together with domain decomposition. I use gromacs2016.3. It seems that this issue should be solved for 2016

Re: [gmx-users] Gromos54a7 electrostatics interactions ?

Hi, Everything looks ok in your mdp's to me. I'm assuming you are using 298 K as you are looking at something like POPC? With both Berger and the 54A7/Poger force fields you shouldn't use non-PC lipids unless you really know what you are doing. A few other things worth noting: Be aware that

Re: [gmx-users] New files after simulation run

On Mon, Sep 25, 2017 at 3:13 PM, Deep kumar wrote: > Hi All, > > I have run an extended simulation for 90ns like this: (my previous run was > for 10ns) > > grompp -f new.mdp -c old.tpr -o new.tpr > I am not very sure about this step.. But instead you can use the

[gmx-users] wall time for every 1000 steps in simulation - reg

Hi, Is it possible to get actual wall time (0 to total time) every 1000 steps, instead of expected time? thanks Meagha -- 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

[gmx-users] New files after simulation run

Hi All, I have run an extended simulation for 90ns like this: (my previous run was for 10ns) grompp -f new.mdp -c old.tpr -o new.tpr mdrun -s new.tpr -cpi old.cpt I output mdrun STDOUT to an output file and it looks like this: ## Back Off! I just

Re: [gmx-users] Gromos54a7 electrostatics interactions ?

Thanks again for your reply and all the info that I've read with great interest! I would like to simulate lipid bilayers that contain my molecules and have a look at my molecules' location and orientation as well as how they can affect lipids properties. My plan would be to try two different

[gmx-users] Simulation in NPgT ensemble

Dear Gromacs users! I wonder to ask whether is possible to perform simulations in NPgT ensemble with the explicit definition of the surface tension value. My system is composed of the lipid bilayer solvated in water. I have found that switching compressibility along x-y to zero and introducing