[gmx-users] Reproducibility of a PMF plot

Dear all, Of course it is always good to prove that a MD simulation is reproducible by repeating several replicas of a simulation and then average over the quantity of interest, specially for a publishable result. I wonder if that also is necessary for a potential of mean force (PMF) calculation

Re: [gmx-users] positive potential energy

Den 2020-03-15 kl. 20:53, skrev Afsane Farhadi: hi all I generated a box 4×4×4 (nm) with 100 molecules methyldiethanolamine by insert-molecules , forcefield is opls . after energy minimization the potential energy decreased  but had a positive value . is my simulation wrong ? help me please

[gmx-users] positive potential energy

hi all I generated a box 4×4×4 (nm) with 100 molecules methyldiethanolamine by insert-molecules , forcefield is opls . after energy minimization the potential energy decreased  but had a positive value . is my simulation wrong ? help me please Sent from Yahoo Mail on Android -- Gromacs Users

[gmx-users] Fatal error: Too many warnings (3) ; WARNING * [file lig.prm, line **] :: How to overcome this error -> simply delete the lines which give warnings?

Dear all, How to overcome this error ? How to overcome this error. Simply delete the lines which give warnings? *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* The above command returns following 'error message' while using with " ions.mdp " This run will generate

[gmx-users] "No atom pairs for dispersion correction" Warning from GROMACS 2020 mdrun

Hello All, I am performing a gpu accelerated simulation on a 292683 atom system (a solvated multimeric protein) using the amber99sb-ildn forcefield. Grompp does not throw any errors or warnings. However, mdrun throws the following warning prior to simulation: WARNING: There are no atom pairs

Re: [gmx-users] Regarding REMD using gromacs4.5.5

Hi Amit Could you please send me your mdp file for implicit solvent remd? Many thanks On Thu, Mar 5, 2020 at 5:07 AM Amit Kumar wrote: > *Message sent from a system outside of UConn.* > > > Thank You Daniel Burns, > Actually, right now I am looking at the installation and trying to install >

Re: [gmx-users] potential energy doesn't have negative value

Den 2020-03-15 kl. 00:59, skrev Justin Lemkul: On 3/14/20 7:15 PM, Afsane Farhadi wrote: I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the