Re: [gmx-users] Replicate a structure

2020-03-09 Thread Bratin Kumar Das
Gmx editconf you can use with -translate flag...after that merz the coordinates of two water droplets. I hope this may help you. On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < devargyachakraborty@gmail.com> wrote: > I have an equilibrated droplet of water. What I want to do is

[gmx-users] Replicate a structure

2020-03-09 Thread Devargya Chakraborty
I have an equilibrated droplet of water. What I want to do is replicate that droplet in the x direction. So that my simulation box will carry two water droplets. Is that possible in gromacs. If yes please guide me. Thank you Devargya Chakraborty -- Gromacs Users mailing list * Please search the

[gmx-users] Setting a electric field in a simulation

2020-03-09 Thread Mijiddorj B
Dear GMX users, I would like to perform MD simulations of solutions applying electric fields such as the microwave heating process. Is it possible to perform in gromacs? 1. How can I set the external electric field in the simulations? (from the user guide, I understood that I need to set 4

Re: [gmx-users] Troubleshooting Generic Floating Point Exception Errors

2020-03-09 Thread Mark Abraham
Hi, Depends when you see them. From mdrun, you're generally blowing up (see user guide and FAQ list). From tools, maybe your input data is somehow bad (or bad in part, so try different parts), or you ran into a silent size limitation in the code (see if a smaller data set works and if so file a

Re: [gmx-users] Troubleshooting Generic Floating Point Exception Errors

2020-03-09 Thread David van der Spoel
Den 2020-03-09 kl. 20:14, skrev Travis Meyer: Hello all, I am a very new user to GROMACS and MD simulations in general. While going through some tutorials and other test simulations I've been getting some floating point exception errors. I recognize that there are a vast number of problems

[gmx-users] Troubleshooting Generic Floating Point Exception Errors

2020-03-09 Thread Travis Meyer
Hello all, I am a very new user to GROMACS and MD simulations in general. While going through some tutorials and other test simulations I've been getting some floating point exception errors. I recognize that there are a vast number of problems that could be causing this - I am not looking for

Re: [gmx-users] ERROR 1 [file lig.prm, line 49] - Can I use the the mdp files -> em.mdp followed by em_real.mdp used for Gromacs 5.1.4?

2020-03-09 Thread Justin Lemkul
On 3/9/20 7:10 AM, Adarsh V. K. wrote: Dear all, How to solve this error ? gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1 The command returns following errors while suing ions.mdp - NOTE 1 [file ions.mdp] ERROR 1

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 191, Issue 10

2020-03-09 Thread Justin Lemkul
On 3/7/20 2:10 PM, Eduardo Mayo wrote: Hi!, I mean the page http://www.gromacs.org/Downloads/User_contributions/Force_fields has a amber14sb.ff.tar.gz amber14sb_OL15.ff_corrected-Na-cation-params.tar.gz but at the top of the page it is a warning that say "These force fields are provided

Re: [gmx-users] ERROR 1 [file lig.prm, line 49] - Can I use the the mdp files -> em.mdp followed by em_real.mdp used for Gromacs 5.1.4?

2020-03-09 Thread Sotirios Dionysios I. Papadatos
In most cases this means that the exact same line is given more than once. I would start from there. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Adarsh V. K. Sent: Monday, March 9, 2020 1:26 PM To:

Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

2020-03-09 Thread Szilárd Páll
Hi Andreas, Sorry for the delay. I can confirm the regression. This affects the energy calculation steps where the GPU bonded computational did get significantly slower (as a side-effect of optimizations that mainly targeted the force-only kernels). Can you please file an issue on

[gmx-users] Clarification on the "-surface" and "-output" options of "gmx sasa"

2020-03-09 Thread ZHANG Cheng
Dear Gromacs, There seems to be very little explanation on the "-surface" and "-output" options of "gmx sasa": -surface: This should always consist of all non-solvent atoms in the system. The area of this group is always calculated -output: can specify additional selections, which should be

Re: [gmx-users] Gromacs 2020

2020-03-09 Thread Mark Abraham
Hi, The code is tested extensively on a range of compilers, so we believe it is correct and compliant. In particular, you're using gcc 6.1.0 and GROMACS tests with 6.4.0, so the issue might have been fixed in the meantime. As newer versions of gcc and cuda will give better performance, I suggest

Re: [gmx-users] Negative Pressure during equilibration

2020-03-09 Thread Mark Abraham
Hi, Check out the GROMACS FAQs - this question is a very frequent one! :-) Mark On Mon, 9 Mar 2020 at 11:42, Sadaf Rani wrote: > Dear Gromacs users > > I am running a free energy test calculation and using position restraints > for all of the system. At the end of pressure equilibration I am

[gmx-users] Negative Pressure during equilibration

2020-03-09 Thread Sadaf Rani
Dear Gromacs users I am running a free energy test calculation and using position restraints for all of the system. At the end of pressure equilibration I am getting negative average pressure as below:- Energy Average Err.Est. RMSD Tot-Drift

[gmx-users] Gromacs 2020

2020-03-09 Thread Turega, Simon
Hi all After attempting to install GROMACS 2020 on new system, I get the error below. The system details & other details are below the error. cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/home/b5018993/src/gromacs-2020 -DCMAKE_C_COMPILER=gcc