Re: [gmx-users] Damping for pulled group

Code issues can be discussed on the gmx-developers mailing list. Feature requests can be made on redmine.gromacs.org. The best case is to file the feature request, take it on yourself, and discuss any issues on gmx-developers :) Thanks. Posted: http://redmine.gromacs.org/issues/2218 I hav

Re: [gmx-users] Damping for pulled group

On 7/18/17 4:44 PM, Alex wrote: Hi all, This is more of a question about where I should make a suggestion for the developers. It turns out that Gromacs pull code was designed nearly perfectly to do simulated friction force microscopy (FFM), i.e. scanning a surface with a tip. The only thing th

Re: [gmx-users] Ethanol energies with CHARMM ff

On 7/18/17 1:28 PM, Sonia Milena Aguilera Segura wrote: Dear GROMACS users, I am running a 4 nm box of ethanol and once I finished the MD, I got the right T, P, density. However, I noticed that my energies are odd. After several trials with different parameters and box sizes I am getting a Tot

Re: [gmx-users] Using nose-Hoover thermostat with berendsen barostat

On 7/18/17 9:23 AM, jay patil wrote: The reason for using berendsen is: I thought parrinello is sensitive, it's not wise to use it while equilibrating. So I was trying to use berendsen for equilibration and then production run with parrinello. One more thought, my system is not well equilibra

Re: [gmx-users] Regarding pdb2gmx and mdrun

On 7/18/17 8:15 AM, S M Bargeen Turzo wrote: Hey I have been trying to convert S100A8A9(has two chains) to .gro but after energy minimization I am not getting an integer for the total charge of the system. What is the magnitude of this non-integer charge? Did you do anything funny during p

Re: [gmx-users] nitrogen itp file with virtual site

On 7/17/17 3:39 PM, Ali Ahmed wrote: Dear Justin Here is the topology file I wrote. I included all the parameters rather than use a specific FF. Thank you for your support ..

Re: [gmx-users] Equilibration of Lipid Bilayers created through charmm-gui

On 7/17/17 2:14 PM, Nidhin Thomas wrote: Hello everyone, I have created an 'alpha-helix protein embedded in a lipid bilayer’ system using charmm-gui. I used the mdp files provided by charmm-gui directly without changing the number of steps or constraints for equilibration. I ran final simu

Re: [gmx-users] Regarding calculation of coordination number

2) to calculate it yourself you integrate the area under the g(r) curve between the two minima and multiple that by the atomic density. Easy to do, even can do in a spreadsheet such as Excel. https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions#Coordination_Numbers Try

Re: [gmx-users] Best Force Field For Gases at High pressure

Check the literature . https://scholar.google.com.au/scholar?q=molecular+dynamics+simulation+of+gases+at+high+pressure Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas

[gmx-users] Fwd: gmx select querry

Date: Mon, Jul 17, 2017 at 11:26 AM Subject: gmx select querry To: Discussion list for GROMACS users Hello All, I have a question regarding the usage of gmx select. I want to select water molecules in a particular subset in z-direction (example z > 5 and z < 10) for each frame of my trajecto

Re: [gmx-users] Damping for pulled group

I mean would it be hard to add a damping term. Sorry, half asleep. :) Alex On Tue, Jul 18, 2017 at 2:44 PM, Alex wrote: > Hi all, > > This is more of a question about where I should make a suggestion for the > developers. It turns out that Gromacs pull code was designed nearly > perfectly to do

[gmx-users] Damping for pulled group

Hi all, This is more of a question about where I should make a suggestion for the developers. It turns out that Gromacs pull code was designed nearly perfectly to do simulated friction force microscopy (FFM), i.e. scanning a surface with a tip. The only thing that's missing is that the equation of

[gmx-users] Ethanol energies with CHARMM ff

Dear GROMACS users, I am running a 4 nm box of ethanol and once I finished the MD, I got the right T, P, density. However, I noticed that my energies are odd. After several trials with different parameters and box sizes I am getting a Total Energy between -1.2 to 0.6 KJ/mol (already normalizae

[gmx-users] Regarding calculation of coordination number

Hello, i have calculated the radial distribution function through the commands as:- gmx rdf -f ab.ttr -s ab.tpr -n ab.ndx -o rdf_ab.xvg -ref x -sel y -cn cn_ab.xvg 1] my doubt is tht whether -cn option is calculating the co-ordination number ie., running coordination number [N(r)] or just the coor

[gmx-users] Best Force Field For Gases at High pressure

Hello GROMACS users Does anyone have an idea about the suitable force field for gases (Methane, Oxygen, and Nitrogen) at high pressure (above 300 bar)?. I have tried with most of the force fields in GROMACS but the physical properties were far from the experimental values. Thank you in advance --

Re: [gmx-users] Using nose-Hoover thermostat with berendsen barostat

The reason for using berendsen is: I thought parrinello is sensitive, it's not wise to use it while equilibrating. So I was trying to use berendsen for equilibration and then production run with parrinello. One more thought, my system is not well equilibrated, I know because it got disturbed wh

Re: [gmx-users] Using nose-Hoover thermostat with berendsen barostat

Hi Mark, Currently I am struggling with equilibrating the system. I am constraining a water molecule in a Bilayer at a fixed distance from the COM of the Bilayer. I tried many things like changing pressure coupling, temp coupling, varying time constants, rlist, varying step size, increasing warn

[gmx-users] Regarding pdb2gmx and mdrun

Hey I have been trying to convert S100A8A9(has two chains) to .gro but after energy minimization I am not getting an integer for the total charge of the system. Secondly when I try to do molecular dynamics simulation using these parameters: ; 0.5 ps NVT production with Langevin thermostat and GB

Re: [gmx-users] CHARMM force file error in gromacs

Hi, The list cannot accept attachments. What did you to try to understand why the pair of files that you think match do not match for the program? Mark On Tue, 18 Jul 2017 09:19 Vikram Dalal wrote: > Hi everyone, > > > I have to do molecular dynamics simulation of a zinc containing protein. >

Re: [gmx-users] Using nose-Hoover thermostat with berendsen barostat

Hi, The more Berendsen you use, the less physics you get ;-) Mark On Tue, 18 Jul 2017 13:44 jay patil wrote: > Hi Experts, > Can we use nose-Hoover thermostat in combination with berendsen barostat. > When I use grompp command, it gives warning berendsen will not give true > ensemble, and with

[gmx-users] Using nose-Hoover thermostat with berendsen barostat

Hi Experts, Can we use nose-Hoover thermostat in combination with berendsen barostat. When I use grompp command, it gives warning berendsen will not give true ensemble, and with -maxwarn 1 option I am able to run the simulation. My doubt is: can we use this combination of thermostat and barosta

[gmx-users] CHARMM force file error in gromacs

Hi everyone, I have to do molecular dynamics simulation of a zinc containing protein. I have kept the Zn molecule along with the protein and generate the topology file by using CHARMM36 force field in Gromacs5.1.4. I have downloaded the CHARMM36 force field from this link:- http://mackere