[gmx-users] GROMACS 2018.x installation

Hi all: I am having trouble installing gromacs-2018.x (x = 1 to 3) on Ubuntu 18.04.  I invoked cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on on a simple i7-7700 machine with a GTX-970 GPU.  In both cases, everything went until make check, at which point a series

[gmx-users] Drude polarization ff for Ca2+ and Mg2+

Dear GMX users, I am wondering where I can find the polarization parameter for Ca2+ and/or Mg2+ for Gromacs? Best, Xianchi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.grom

Re: [gmx-users] Documentation on gmx densorder?

Hello Micholas and David, If possible, could this discussion be kept on the list. I was unaware of this tool and would like to know about "gmx densorder" input, output, and usage. If not, would it be OK if I sent my own followup questions to Micholas or David in an independent email? David, tha

[gmx-users] bk3 water energy minimization potential shift

Hello, I would like to run the BK3 water model on gromacs. I am using a table to run this model due to the gaussian charges and buckingham potentials, with group cutoff scheme. I think I need to use the 'Potential-shift' coulomb-modifier to prevent some artificial forces due to discontinuity at

Re: [gmx-users] (no subject)

*Please remember (its your query to me )* Hi, Can you please share a link to something that indicates why this would be a good tool for modeling such experimental pulling scenarios? Making the case for implementing such a feature would benefit from that. Mark >

Re: [gmx-users] force/time application for pull

It will be useful for all candidate including me those who don't want to go for calculating PMF but just want to study the stability of the simple nucleic acid with drugs (ICL) or with protein+dsDNA or DNA aptamer etc. during the structural transition. Where rupture of dsDNA or unzipping of dsDNA

Re: [gmx-users] (no subject)

Dear mark I had already discussed regarding force/extension protocol. But I didn't get any response from your side. I dont have idea to upload some pictures. On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham wrote: > Hi, > > The list cannot accept attachments. Upload to a file sharing service and >

Re: [gmx-users] (no subject)

Hi, The list cannot accept attachments. Upload to a file sharing service and share a link. We will likely need more background information also. Mark On Fri, Aug 31, 2018, 12:22 Rakesh Mishra wrote: > Hi every body > can any one explain what is the mean of this graph > obtained from gromacs

Re: [gmx-users] Documentation on gmx densorder?

Thanks you for directing me to the paper. Before I switch to off-line questions, do you recall what his inputs needed to be? I keep getting the error: " Program: gmx densorder, version 2016.3 Source file: src/gromacs/gmxana/gmx_densorder.cpp (line 808) Fatal error: No or not correct number (

Re: [gmx-users] force/time application for pull

It can take time to read through papers. A title, link and a short summary would be helpful to understand what the benefit would be. In particular whether you just need information to add the functionality for your use case or whether enough people other would use the extra functionality you re

[gmx-users] Optimal pme grid

Hi It seems that changing the number of ntmpi and ntomp affects the number of steps that takes to calculate the optimal pme grid. Is that correct? Please see the following output gmx mdrun -nb gpu -ntmpi 1 -ntomp 16 -v -deffnm nvt Using 1 MPI thread Using 16 OpenMP threads step 2400: timed with

[gmx-users] (no subject)

Hi every body can any one explain what is the mean of this graph obtained from gromacs constant velocity pulling of dsDNA along the helical direction. (force.xvg). Basically sudden drop of force represents what ? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.o

[gmx-users] (no subject)

Hi every body can any one explain what is the mean of this graph obtained from gromacs constant velocity pulling of dsDNA along the helical direction. (force.xvg). Basically sudden drop of force represents what ? -- -- Gromacs Users mailing list * Please search the archive at http://www.grom

Re: [gmx-users] Documentation on gmx densorder?

Den 2018-08-30 kl. 15:34, skrev Smith, Micholas D.: Dear GMX users, I was wondering if anyone has used the gmx densorder (originally g_densorder) in the past utility in the past. I have system with an interface and the idea of " gmx densorder reduces a two-phase density distribution along an

Re: [gmx-users] force/time application for pull

Dear Dr. Justin Ultimately Mark has not replied . Can you please tell me what this peak is revealing. hear 3' of one strand is fixed and 3' of another strand is pulled along the helical direction of dsDNA (12 bp). using constant velocity pulling using your protocol of umbrella sampling (output f/t