Re: [gmx-users] topogen usage

On 8/2/18 7:36 PM, paul buscemi wrote: Dear Users, Although topogen is a bit dated it seems to work well for ‘smaller’ polymers -500 atoms- and builds a single file itp. However in making a file for nylon 12 1000 atoms , a ‘central’ itp was create and separate files were made for

Re: [gmx-users] constant pressure in NPT simulation

On 8/3/18 3:57 AM, Quyen V. Vu wrote: Hi, please check this: http://www.gromacs.org/Documentation/Terminology/Pressure Usually, if your system contains more than one element, use one thermostat and barostat for solvent, one for the solution will give you more precise instead of group system

Re: [gmx-users] Question about water insertion

Hi, You can play around with the -radius and -scale parameters if you're getting clashes you don't like. However, it seems like you really should be using gmx solvate. You could accomplish your goal with "gmx solvate -cs tip4p.gro -box 10.1103 10.34753 3.958 -maxsol 13853" Kevin On Fri,

Re: [gmx-users] GROMACS Installation error on domdec.cpp

What version of MPI do you have? It may be helpful to indicate exact location of MPI if the paths are not automatically found. On 08/03/2018 02:43 PM, 郭聪 wrote: Hi All, I wanted to build GROMACS-2016.4 on hpc clusters but I got error with domdec.cpp. Could anyone helps me with that?

[gmx-users] GROMACS Installation error on domdec.cpp

Hi All, I wanted to build GROMACS-2016.4 on hpc clusters but I got error with domdec.cpp. Could anyone helps me with that? Thanks! ps: I succeeded to build it on my lab pc. I am wondering if something is wrong with GROMACS code or the compiler. I used gnu and openmpi. tar -zxvf

[gmx-users] Question about water insertion

I have one water molecule in my gro file as below: TIP4P 4 1SOL OW1 0.054 0.005 0.022 1SOLHW12 0.009 0.072 0.073 1SOLHW23 0.142 0.041 0.008 1SOL MW4 0.060 0.018 0.026 0.00 0.000 0.000

Re: [gmx-users] constant pressure in NPT simulation

Hi, please check this: http://www.gromacs.org/Documentation/Terminology/Pressure Usually, if your system contains more than one element, use one thermostat and barostat for solvent, one for the solution will give you more precise instead of group system for all On Fri, Aug 3, 2018 at 2:14 PM

Re: [gmx-users] constant pressure in NPT simulation

I think calling this community "customers" is very funny. ;) Pressure fluctuations depend on the system composition, size its starting state (how well and for how long it was equilibrated), and many other things. Further, pressure is not supposed to be dead-on constant and some degree of

Re: [gmx-users] constant pressure in NPT simulation

Hello, what do you mean with the pressure not being constant? If you mean the fluctuations in the instantaneous pressure, this is normal. What should be constant is the time average of the pressure over the time of the simulation. I don't see anything particular in your mdp file that could

[gmx-users] constant pressure in NPT simulation

Dear all customers. I have a problem, in my NPT simulations the pressure is not constant and the temperature is. Earlier simulation in NVT conditions was ok. I use these parameters: tcoupl = nose-hoover tc_grps = system tau_t = 0.002 ref_t

[gmx-users] Molecules in micelles

Dear Gromacs Users, My system contains two micelles. In order to calculate the radius of gyration for two micelles, I need to select molecules in each micelle. Is there any tool available in Gromacs to do that? If available, what options in the -h should I use to get the information I want.