Re: [gmx-users] Umbrella Sampling - Pulling distance larger 0.49 times box size Error during NPT equilibration

On 7/4/18 6:51 AM, Chenlin Lu wrote: Dear gromacs users, Hello, I am doing umbrella sampling to calculate the PMF puling an Au ion out of a protein channel. Basically, I followed the procedure given by Justin's tutorial. The configuration generation was finished correctly and the .mdp file

Re: [gmx-users] question regarding high temperature simulation in Gromacs

On 7/4/18 4:08 PM, Quyen V. Vu wrote: Dear Prof. David, Could you kindly describe in more detail for give me references which problems will happen? What happens when you boil water? It turns to steam and its volume expands rapidly. That behavior is not very stable for most barostats.

Re: [gmx-users] freezing or constraining

On 7/4/18 5:52 PM, Dallas Warren wrote: Freezing means that the atoms are not able to move. Constrained means that the atoms can move around a certain point, there is some movement possible. Not quite - though historically people have used "constrain" and "restrain" interchangeably,

Re: [gmx-users] freezing or constraining

Freezing means that the atoms are not able to move. Constrained means that the atoms can move around a certain point, there is some movement possible. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal

Re: [gmx-users] question regarding high temperature simulation in Gromacs

Dear Prof. David, Could you kindly describe in more detail for give me references which problems will happen? On Wed, Jul 4, 2018, 15:13 David van der Spoel wrote: > Den 2018-07-04 kl. 09:11, skrev Dr. Puspita Halder: > > Hi All, > > > > I have been recently using Gromacs 5.1.4 version for

Re: [gmx-users] question regarding high temperature simulation in Gromacs

Hi, Thanks for your reply. I'd try to run my high temperature simulations with pressure coupling off as per your suggestion. I was wondering about the simulation parameters (as mentioned in the early post) that I need to change for running high temperature simulations and should I use

[gmx-users] Umbrella Sampling - Pulling distance larger 0.49 times box size Error during NPT equilibration

Dear gromacs users, Hello, I am doing umbrella sampling to calculate the PMF puling an Au ion out of a protein channel. Basically, I followed the procedure given by Justin's tutorial. The configuration generation was finished correctly and the .mdp file summary_distance.txt are shown below:

Re: [gmx-users] Potential energy reported by gmx energy command

Den 2018-07-04 kl. 11:19, skrev atb files: Thanks Prof. David, now my energies are making some sense and they are following the trend that, with increase in particle number RMSD decreases by (N)^1/2 for LJ fluid. If -nmol option is available, which may be used to calculate per particle averages,

[gmx-users] gmx genion -neutral adds some opposite charge under some conditions

Hi, My system has non-zero total charge: 34.09. I do gmx genion -neutral on it, I get 35 CL ions dumped into it. So I continue to get warning "System has non-zero total charge: -0.91". Fell free to try with your own system. I think this should be fixed. -- Gromacs Users mailing list *

Re: [gmx-users] Potential energy reported by gmx energy command

Thanks Prof. David, now my energies are making some sense and they are following the trend that, with increase in particle number RMSD decreases by (N)^1/2 for LJ fluid. If -nmol option is available, which may be used to calculate per particle averages, why default unit of "KJ/mol" has been

Re: [gmx-users] question regarding high temperature simulation in Gromacs

Den 2018-07-04 kl. 09:11, skrev Dr. Puspita Halder: Hi All, I have been recently using Gromacs 5.1.4 version for simulating my protein systems (mainly prion protein and some of its mutants). I'd like to perform high temperature (400K or 500K) simulations with those. Now my question is what

[gmx-users] question regarding high temperature simulation in Gromacs

Hi All, I have been recently using Gromacs 5.1.4 version for simulating my protein systems (mainly prion protein and some of its mutants). I'd like to perform high temperature (400K or 500K) simulations with those. Now my question is what should be the values of the simulation parameters e.g.,

[gmx-users] RV: Error energy minimization: No such moleculetype NA

Hi Mark, I have used the changed .top for the grompp. Besides, in the .top file I have writen: ; Include topology for ions #include "gromos43a1.ff/ions.itp" I have checked the "ions.itp" of the gromos43a1.ff folder and NA is included. What else can I do? Best, C. -Mensaje

Re: [gmx-users] 500ns simulation

Increase the number of steps On Wed, 4 Jul 2018, 12:07 pm Quyen V. Vu, wrote: > Take simulation time= timestep (dt) * number of steps (nstep) > > On Wed, Jul 4, 2018, 12:48 Soham Sarkar wrote: > > > Change in the number of time steps > > > > On Wed, 4 Jul 2018, 10:54 am Raag Saluja, wrote: >

Re: [gmx-users] 500ns simulation

Take simulation time= timestep (dt) * number of steps (nstep) On Wed, Jul 4, 2018, 12:48 Soham Sarkar wrote: > Change in the number of time steps > > On Wed, 4 Jul 2018, 10:54 am Raag Saluja, wrote: > > > Hi! > > > > What changes do I make to the mdp files provided by you in the lysozyme > >

[gmx-users] Generating N2 topology

Hi All, I'm currently trying to generate the topology for molecular Nitrogen (N2) and am running into some trouble. For reference, the pdb file I have for N2 is as follows: HETATM1 N6B HDZ 0 0.000 0.000 0.553 1.00 0.00 N HETATM2 N6A HDZ 0 0.000