Re: [gmx-users] Charmm to Gromacs itps

@Justin, thank you Justin. I will give it a try then. @Miro, sure, I will look into it, thank you. - Yogesh On Fri, 31 Jan 2020 20:24:36 +0530 Miro Astore wrote Would topotools in vmd not work in this context? I haven't used it but readabout it recently a

[gmx-users] Energy plots for specific atoms/selections

Hi, I want to get an xvg file that will show me the LJ, Coulomb, and dihedral energies on a specific set of atoms. I've tried passing a .dat file with the groups of atoms from gmx select to gmx enemat but I get an error message saying that I must not have included those groups in my mdp file. How

[gmx-users] High energies after alignment of trajectory

Hi, I want to calculate the free energy difference of turning some position restraints on. Therefore I run two MD simulations, one with the restraints on the protein turned on (I’m restraining the backbone of a specific loop), in the other one I have the restraints turned off. Then I rerun the

Re: [gmx-users] gromacs-2020 build gcc/nvcc error

Dear Ryan, On Thu, Jan 30, 2020 at 11:31 PM Ryan Woltz wrote: > Dear Szilárd, > > Thank you so much for your help. I performed the following steps > and it seems to have built successfully, I'll let you know if it does not > run correctly as well. > > rm -r gromacs-2020/ > sudo apt-get

Re: [gmx-users] Charmm to Gromacs itps

Would topotools in vmd not work in this context? I haven't used it but read about it recently and it would seem this is the use case. Of course you also need parameters. Wondering. Best, Miro Le sam. 1 févr. 2020 à 00:55, Justin Lemkul a écrit : > > > On 1/31/20 8:25 AM, atb files wrote: > > >

Re: [gmx-users] Charmm to Gromacs itps

On 1/31/20 8:25 AM, atb files wrote: The files are given on the following server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated systems using NAMD. If the individual topologies are not available anywhere, just a PSF, then you will have to

Re: [gmx-users] How to use TIP4P-ICE water model

Hi, I did not fully understand what you have done. But my suggestion will be to use the pre-build tip4p.gro to build the water box and then perform the simulation with the topology of tip4p-ice and run long enough to allow the molecular system to relax, then check RDF. If the profile is not what e

Re: [gmx-users] Charmm to Gromacs itps

The files are given on the following server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated systems using NAMD. -Yogesh On Thu, 30 Jan 2020 19:45:16 +0530 Justin Lemkul wrote On 1/28/20 3:35 AM, atb files wrote: > > >

Re: [gmx-users] Cell Membrane Potential

Hi Frank, I have never conducted any simulation on membrane potential, but you reminded me of the fact that many molecular dynamics simulations on membrane proteins do not consider the membrane potential which is ubiquitous and versatile in biological environment. If the membrane potential i

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 189, Issue 80, 2. Re: Analysis with .sh file (Li, Shi)

Dear all, This is an example of a line I have been using on Gromacs 5.0.4:" echo "10" "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &" and this is the error message I'm receiving from Gromacs: "Error in user input: Invalid selection '10 12 ' B Near '12' B B B synta