[gmx-users] Free energy perturbation of ligand

Hello, I am trying to calculate FEP using gromacs. I have used pmx for initial structure and .itp file. I am getting the following warning WARNING 1 [file MOL.itp, line 185]: Some parameters for bonded interaction involving perturbed atoms are specified explicitly in state A, but not B -

Re: [gmx-users] simulation on graphite sheet

Hi, On Tue, Feb 11, 2020 at 2:13 PM Devargya Chakraborty < devargyachakraborty@gmail.com> wrote: > Hello, > I was thinking of simulating a liquid on graphite surface and have made a > system but couldnt simulate it. while doing the nvt simulation, after some > time i am getting lincs error.

[gmx-users] density map calculation of lipid around 10 angstrom of protein

hello i am trying to calculate 2D number-density maps of lipid around 10 angstrom of protein. My system consist both coarse grained protein and lipid (using martini force field).the command is gmx densmap -f *.xtc -s *.tpr -n *.ndx -aver z -bin 0.02 -xmin -1 -xmax -1 -o *.xpm but the error i am

[gmx-users] simulation on graphite sheet

Hello, I was thinking of simulating a liquid on graphite surface and have made a system but couldnt simulate it. while doing the nvt simulation, after some time i am getting lincs error. can anybody help me, if you want i can send you the files. Thanks, Devargya chakraborty PhD scholar

[gmx-users] Python API Documentation question

Hello As I'm quite new to both gromacs in and of itself and the python API I'm struggling a bit figuring out how to go about getting simulations running using the API. I've managed to write a Python script creating and running shell command line commands to run through the Lysozyme tutorial,

[gmx-users] Query

Dear Gromacs Experts, I want to parametrize Ferric citrate and have already performed DFT calculations using different basis sets, but I am unable to upload the refined molecule on, ATB so that I can get its topology files to proceed further. Please help. Thanks in advance. Neha. -- Gromacs

[gmx-users] REMD stall out

Hi, I continue to have trouble getting an REMD job to run. It never makes it to the point that it generates trajectory files but it never gives any error either. I have switched from a large TREMD with 72 replicas to the Plumed Hamiltonian method with only 6 replicas. Everything is now on one

Re: [gmx-users] Query

You cannot generate the desired parameters (.itp) for metals in the ATB server. In fact even CGenFF or RED server are also not useful for metals. However, if you have access to any DFT modeling in house to perform QM calculations using Gaussian etc., you can generate/build your own force field for