[gmx-users] Turing GPUs

Any of the developers been able to test the soon to be released Turing GPUs yet? Seems like from a ray tracing perspective should be very good. What about for MD? Thanks Dallas Warren -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] Fwd: free energy calculation.

Can't help directly, but Good primer for doing Gibbs energy calculations and list of references on to read further you can find at : http://www.alchemistry.org/wiki/Main_Page Other place you should be looking is the literature, what have others done and published when doing what you are doi

[gmx-users] Fwd: free energy calculation.

Hi everyone. Kindlt need your help urgently. -- Forwarded message - From: neelam wafa Date: Mon, 27 Aug 2018, 3:41 pm Subject: free energy calculation. To: , Hi! Dear gmx users, I have md simmulations of a protein with four different ligands. now I want to calculate the free en

[gmx-users] re-How to evaluate the Hbond and non-bonded interactions between ligand-receptor

Dear Dr. Quyen and all users Thanks a lot for your replying. How can I determine the most efficient interactions(the Hbond and non-bonded interactions, life time,Hbond occupancy and etc ...) observed during 50 ns molecular dynamic simulations in ssDNA-ligand complex. Using hbond command in groma

[gmx-users] protein dna pulling

Hi, I have been trying to pull a double stranded DNA from protein's binding surface. But I am facing an issue. After defining the pull vector when I apply the pull force the DNA's one stand got pulled completely while other strand partially remain attached ( https://drive.google.com/drive/folders/0

[gmx-users] Parametrization matters

Hello, I would like to know how to make parameters for Mn2+ in Gromos 53a6 force field. I haven't found a paper showing parameters for that force field, just for Amber. With regards, -- *M.Sc. Disraeli Cavalcante Araujo Vasconcelos* *Bacharel em Biotecnologia - Universidade Federal do Ceará* *M

Re: [gmx-users] Calculate and print ALL distances between atoms A and B from structure file (i.e. not over time), with detailed information

On 8/27/18 9:37 AM, Javier Luque Di Salvo wrote: Dear users, I am trying to calculate ALL distances between two types of atoms, say atom A and atom B. The system is a polymer composed of 20 linear chains. Each chain has 1 (one) atom A that can form a crosslink with some atom B of an adjacent,

[gmx-users] Calculate and print ALL distances between atoms A and B from structure file (i.e. not over time), with detailed information

Dear users, I am trying to calculate ALL distances between two types of atoms, say atom A and atom B. The system is a polymer composed of 20 linear chains. Each chain has 1 (one) atom A that can form a crosslink with some atom B of an adjacent, near chain. Thus, in order to generate such crosslink

Re: [gmx-users] [EXT] Re: Density of POPC membrane and lateral diffusion

Thank you Kevin - I will extend the simulation time from 20ns in order to obtain enough sampling. Iris Iris Nira Smith | Postdoctoral Fellow | Genomic Medicine Institute Cleveland Clinic | 9500 Euclid Ave. / NE5-255 | Cleveland, OH 44195 | (216) 445-7885 On 8/21/18, 10:55 AM, "

[gmx-users] GROMACS result not matching with my code

Dear gmx users I am developing a C++ code for simulation of electric double layer. Currently, I am calculating interaction energy of a system of water molecules (TIP4P model) in a cell and checking the results with that of GROMACS. I created a cubic box of size 120 angstroms with 909 molecules at i

[gmx-users] free energy calculation.

Hi! Dear gmx users, I have md simmulations of a protein with four different ligands. now I want to calculate the free energy of binding. which method does suit after md simmulation? either g_mmpbsa or gmx BAR method. If I use BAR method is it necessary to set charges to zero as in the tutorial g

Re: [gmx-users] GMXRC removes trailing colon from existing MANPATH

On Mon, Aug 27, 2018 at 11:18 AM Peter Kroon wrote: > Hi, > > > sorry for the late reply, holidays took priority :) > > I made a redmine issue here: https://redmine.gromacs.org/issues/2628 Thanks. > What change would you like me to submit? I don't have a fix other than > simply appending a co

Re: [gmx-users] GMXRC removes trailing colon from existing MANPATH

Hi, sorry for the late reply, holidays took priority :) I made a redmine issue here: https://redmine.gromacs.org/issues/2628 What change would you like me to submit? I don't have a fix other than simply appending a colon in my bashrc. Peter On 07-08-18 14:45, Szilárd Páll wrote: > Hi, > > C

Re: [gmx-users] Changing Sigma in force field

Hi, Does your topology actually refer to the new atom type? If so, you can prove it by commenting out the definition of the atom type, and see that grompp complains about it. Mark On Wed, Aug 22, 2018 at 4:59 PM hosein geraili wrote: > Dear all,I am trying to change the epsilon of one atom typ