[gmx-users] Bond lengths

Dear Users I have performed a 200 ns MD simulation of a protein and a small molecule inhibitor of 30 atoms, using GROMOS 43a1 ff and Gromacs v 5.0. Taking reference from a number of papers and similar systems, I have used LINCS algorithm to constrain all bond lengths. I have reported interactions

Re: [gmx-users] couple-intramol

Hi, Thanks. If I want to calculate the intramolecular energy of the ligand, I need to choose Coul-14:LIG-LIG, LJ-14:LIG-LIG, Coul-SR:LIG-LIG and LJ-SR:LIG-LIG in the .edr file. Am I wrong? On 4 January 2017 at 04:03, Justin Lemkul wrote: > > > On 1/3/17 2:40 PM, Qasim Pars

Re: [gmx-users] force calculations in PMF

Since I don't use WHAM or even know what it is, I can only guess that feeding pullf data sets the COM force as a function of time. Conversely, GMX reports COM pullf data when pulling is set up via pull code. And that is the pulling force acting upon the COM of the _pulled object_. So, I can

Re: [gmx-users] force calculations in PMF

HI Alex! OK.. :-) Let me try to put it this way. In WHAM method we supply pullf files. I had doubt regarding forces listed in those files. Whether these values are for the entire system or the forces acting on the particular group which is being pulled away. Regards Deepak On Wed,

Re: [gmx-users] force calculations in PMF

There's a reason no one is replying: we can't understand your question. :) On 1/3/2017 8:09 PM, deepak bapat wrote: Dear Gromacs users I had a doubt regarding pull code. Which force values are considered while calculations? ensemble average values of the entire system or the forces acting on

[gmx-users] force calculations in PMF

Dear Gromacs users I had a doubt regarding pull code. Which force values are considered while calculations? ensemble average values of the entire system or the forces acting on the group/atoms under consideration. Regards Deepak -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] couple-intramol

On 1/3/17 2:40 PM, Qasim Pars wrote: Dear users, I got a little bit confused about the use of "couple-intramol". If I set it to "no", the intramolecular intractions of the ligand are "on" when the ligand is decoupled, right? It means that I don't need to set [ More specifically,

Re: [gmx-users] mdrun initialises, fails to run, no error message

On 1/3/17 10:43 AM, Natalie Tatum wrote: Dear all, I'm hoping you can shed light on (a) what my mdrun problem is and (b) where to start fixing it. I'm simulating different mutants of a protein dimer on DNA, for 10 ns a-piece. I have successfully run this protocol on the wild-type protein, on

[gmx-users] couple-intramol

Dear users, I got a little bit confused about the use of "couple-intramol". If I set it to "no", the intramolecular intractions of the ligand are "on" when the ligand is decoupled, right? It means that I don't need to set [ nonbond_params ] part for the ligand? ; Free energy free-energy

Re: [gmx-users] About the number of step in Argon Molecular Dynamic -Phase transition

Hi Mark, Thank you very much for your reply. It seems to me very strange what happens precisely because the equilibria of Temperature and Pressure were realized to me to look with success during time of equilibration of almost 10 ns for the case of NVP that allowed a equilibration of the pressure

[gmx-users] The Rg does not change at all during the umbrella sampling

Dear all, I want to perform pulling simulations on a polymer-drug system. I have performed simulations on polymer and polymer+drug for 30 ns and then set up system for pulling. After generating configurations I chose some of them and performed a 10 ns of MD for each window. However, when I plot

Re: [gmx-users] Reading tpx file (md_0_1.tpr) version 110 with version 100 program

Hi, You can only generate an old tpr format with the version of the code that produced that. So you want to either upgrade the version on your cluster, or install the old version on your laptop for your convenience. Mark On Wed, Dec 28, 2016 at 10:11 PM Zhang, Cheng

Re: [gmx-users] New inGromacs

Hi, We'd be quite happy to consider organizing a GROMACS activity in e.g. Africa if there's a suitable number of users it would help and a way to pay travel expenses. We may have ways to find money, if people have communities they want to expose further to GROMACS. Mark On Thu, Dec 29, 2016 at

Re: [gmx-users] Exploding temp/pressure.

Hi, P-R coupling is only stable if the system is already near equilibrium, so I would always vary other stuff (like step size) while using NVT or Berendsen P coupling (or both in successive stages). Although your observations are consistent with an initial structure that has reached a reasonable

Re: [gmx-users] Exploding temp/pressure.

Did you forget to set an initial temperature distribution? In your mdp you set gen_vel to no. So it will not create an initial velocity distribution matching your temperature. For the first simulation of your workflow, you should set gen_vel: yes and continuation: no. Then for all simulation that

[gmx-users] About GTX-Titan-X(Pascal)

Dear gromacs users. Does the latest version of gromacs support GTX-Titan-X(pascal) or not? It’s code name is GP102-400, different from GTX1080 or GTX1070.(GP104-200 or GP104-400) Thanks a lot. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] About GTX-Titan-X(Pascal)

Dear gromacs users. Does the latest version of gromacs support GTX-Titan-X(pascal) or not? It’s code name is GP102-400, different from GTX1080 or GTX1070.(GP104-200 or GP104-400) Thanks a lot. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] relative reorientation calculation

Dear all Good day. I am working one 36 chain fibril cross section. I want to calculate relative reorientation with respect to the center chain. For my simulation, i use position restrain in the center chain. I am little confused how I calculate relative reorientation (Δφ/Δr). Do I have to