Re: [gmx-users] gmx energy

It is Short Range SR and Total LJ when considering long range tail effects beyond R_cutoff. SR Coulomb and Reciprocal part of it. Find more info in Groamcs Manual! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] How to build a topology file of Gromacs for a system contains two graphene sheet?

It depends whether you are simulating a flexible sheet or fixed wall. For flexible sheet you should define each sheet in one itp file. -- 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] gmx enenrgy

Hi all when we use gmx energy what is the difference between LJ-(SR), LJ-14, Coulomb-14, Coulomb(SR)? those mentioned energies, give us energy interaction of total system. right? if I want to determine interaction enenrgy for example, LJ, between two special species, not in total system, what

[gmx-users] Umbrella Sampling

Hi! I am trying to do umbrella sampling between two 2D-sheets. I did it according bevan lab tutorial the problem I encounter is that after pulling steps. I perform umbrella sampling with rate of 0.0 however, two sheets get back together and initial configuration and final configuration are

[gmx-users] tilt angle for POPC

Dear Gromacs users, I am interested in calculation of tilt angle for the POPC headgroup (angle distribution between the P-N vector and Z axis). I am not sure if my approach is correct as my angle distribution does not seem reasonable. Given a bilayer with 200 lipids (100 lipids in each leaflet

Re: [gmx-users] six member ring won't stay flat

Hi, If you poke your finger into something, it isn't going to stay flat. :-) Mark On Wed, Jan 17, 2018 at 9:44 PM MD wrote: > Hi Mark, > Can you tell me more details about the ring's atoms interacting with an > environment? What interactions did you mean? > Thanks, > Ming >

Re: [gmx-users] potential profile with PBC

Okay, ignore my question. :) I really should have looked at the description of how gmx potential does its job. Switching to -correct fixes the issue, even if this is somewhat fake. Alex On Wed, Jan 17, 2018 at 3:49 PM, Alex wrote: > Hi all, > > I have a perfectly

[gmx-users] potential profile with PBC

Hi all, I have a perfectly well-behaved system that consists of a membrane in water + ions. Upon plotting the per-slice profiles (ion densities and potential: https://www.dropbox.com/s/tl91lg0fu2u5lbc/profiles-1.jpg?dl=0) everything looks great with one exception: the potential values are

Re: [gmx-users] six member ring won't stay flat

Hi Mark, Can you tell me more details about the ring's atoms interacting with an environment? What interactions did you mean? Thanks, Ming On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham wrote: > Hi, > > You still have many sources of problems (e.g. the warnings you

Re: [gmx-users] dielectric constant along specific direction

Den 2018-01-17 kl. 19:39, skrev Iman Ahmadabadi: Dear Gromacs users, Does the gromacs have the ability to compute the dielectric constant along a specific direction (for example x axis)? Sincerely You can easily do that manually from the Mtot.xvg file. Whether it means something is for you

[gmx-users] dielectric constant along specific direction

Dear Gromacs users, Does the gromacs have the ability to compute the dielectric constant along a specific direction (for example x axis)? Sincerely -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] How to build a topology file of Gromacs for a system contains two graphene sheet?

I want to create a topology. top file of gromacs package for a system containing two graphene sheet. Does anyone know how can I make that? Also, I have some questions as follows: 1- Is it need to assign [pair] directive for such system? 2- Are these two sheets should be considered as one compound

Re: [gmx-users] regarding pbc issue

Thank you so much,I've got it now. we know that for example 2 molecule can not stick to each other they just close enough till repulse each other. Now, imagine pulling, if I can not see "really broken" structures in classicalMD , so what would be my criterion and clue to say that:"that's

Re: [gmx-users] Electron density using g_density

Hi All, I did a short test on this. Following is the results. I made two electron.dat files, one like: 1 N = 7 and the second one like: 2 N = 7 N = 7 I also made an index.ndx with these groups: r lipid1 & a N r lipid2 & a N Next, I calculated the electron density for these two groups using

Re: [gmx-users] Gromacs 2016.3 orte error while running on cluster

HI! WORKS LIKE A CHARM NOW. Thank you for your hints! .-) Am 17.01.2018 um 13:04 schrieb Rainer Rutka: HI! Just a question. We try to start a MPIed job with Gromacs 2016.3 on our cluster-system here in Germany. Unfortunately we get this error: An ORTE daemon has unexpectedly failed after

Re: [gmx-users] Electron density using g_density

Hi Gromacs users, My system is composed of three lipid molecules. When I made the topology file for new lipids in the system, I chose some atom names by my choice. Now, when I want to make an "electron.dat" file which includes the atomic number for each atom name in the system, I have more than

Re: [gmx-users] regarding pbc issue

On 1/17/18 11:23 AM, Rose wrote: I mean, sometimes structures may really break or collapse, in these situations trjconv won't show these broken structures whole yes? just will show them broken (as they really are) yes? In the context of the question I was answering, "broken" means that it

Re: [gmx-users] regarding pbc issue

I mean, sometimes structures may really break or collapse, in these situations trjconv won't show these broken structures whole yes? just will show them broken (as they really are) yes? Sent from my iPhone > On Jan 17, 2018, at 18:15, Justin Lemkul wrote: > > > >> On

Re: [gmx-users] regarding pbc issue

On 1/17/18 9:40 AM, Rose wrote: You mean if -pbc could make molecule whole,everything is ok, but if not it means the molecule was broken from first, yes? mdrun writes "broken" coordinates because the physics does not depend on our visualization convenience. Most programs account for PBC.

Re: [gmx-users] regarding pbc issue

You mean if -pbc could make molecule whole,everything is ok, but if not it means the molecule was broken from first, yes? Sent from my iPhone > On Jan 17, 2018, at 16:19, Justin Lemkul wrote: > > > >> On 1/17/18 5:51 AM, Vidya R wrote: >> Hi Justin, >> >> I got the same

Re: [gmx-users] six member ring won't stay flat

​Hi! You are completely right about the parametrization. I found the pyrodoxal in charmm and I think I am going to start over to combine it with lys which can reduce input from outside source to make charmm happy. however I left the md.mdp run yesterday and this morning i found the methyl group is

Re: [gmx-users] six member ring won't stay flat

On 1/17/18 9:35 AM, MD wrote: Hi, so yesterday I left it moving forward to do the md.mdp. Very strangely, the ring goes back to flat form after md.mdp. I am not quite sure what happened here? As I said yesterday, the topology you generated was based on incorrect structure and inappropriate

Re: [gmx-users] six member ring won't stay flat

Hi, so yesterday I left it moving forward to do the md.mdp. Very strangely, the ring goes back to flat form after md.mdp. I am not quite sure what happened here? Ming On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham wrote: > Hi, > > You still have many sources of problems

Re: [gmx-users] Gromacs 2016.3 orte error while running on cluster

Hi, This is an error emitted by hwloc library that GROMACS uses (and OpenMPI too). As there is no indication of other errors, as the message states you can disable it with the HWLOC_HIDE_ERRORS variable which should allow the run to start. You could also recompile GROMACS with a more recent

Re: [gmx-users] Rupture force definition

On 1/17/18 7:09 AM, Rakesh Mishra wrote: Dear, ​Justin​ I have one query regarding pulling of si-rNA (having chain-a and chain-b). Here, I am pulling 3' end of chain-a and fixed 3' end of chain-b (diagonally apposite ). I am doing pulling using gromacs with constant velocity rate using

Re: [gmx-users] regarding pbc issue

On 1/17/18 5:51 AM, Vidya R wrote: Hi Justin, I got the same result as you said. What confused me was, when I viewed movie.pdb file generated by the following command, gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n index.ndx -o movie.pdb two hydrogen molecules of

[gmx-users] Rupture force definition

Dear, ​Justin​ I have one query regarding pulling of si-rNA (having chain-a and chain-b). Here, I am pulling 3' end of chain-a and fixed 3' end of chain-b (diagonally apposite ). I am doing pulling using gromacs with constant velocity rate using Umbrella sampling. after finalization of pulling

[gmx-users] Gromacs 2016.3 orte error while running on cluster

HI! Just a question. We try to start a MPIed job with Gromacs 2016.3 on our cluster-system here in Germany. Unfortunately we get this error: An ORTE daemon has unexpectedly failed after lunch... See more in the attached gromacs-run-error.txt file. Our submit-script is attached, too:

Re: [gmx-users] regarding pbc issue

Hi Justin, I got the same result as you said. What confused me was, when I viewed movie.pdb file generated by the following command, gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n index.ndx -o movie.pdb two hydrogen molecules of my organic compound, were unbonded to