please guide me
hi. i run adfr for docking purpose but give permission denied error and i dont know how can i resolve it please guide me.
04 May 2018 1,390 1 View
i play simulation and for review of fluctuation and must view xpm file and use from xview for this file but this program unsupported image type.how i can this type file?
31 December 2017 5,445 0 View
hi i play simulation by gromacs. i run nvt and npt and my system equilibrate. how can i understand my simulation how much time need?
31 December 2017 5,801 3 View
hi i play MD simulation but, between temperature of nvt and npt is different.is this normal? if no whats factor of this? and why in this pictures rmsd in nvt is different to rmsd in npt state?
31 December 2017 1,080 5 View
salaam dostan man danshjoye olompezeshki tehran hastam mikham bebinam kodom ostad dakhel kodom daneshgah dar tehran gromacs ra dars mide khastam beram sare klasesh?
31 December 2017 7,366 0 View
for secondary structure analysis by gromacs 5.07 i need to install dssp but i dont know how i can install .please guide me
31 December 2017 6,039 4 View
hi i need to some vector which contain signal peptides for example ompA or pELB IN SNAP GENE.
09 October 2017 1,773 0 View
replication suppress is a method for increase of protein expression.i need articles for review of this topic.Please send to me everything associated with it
05 June 2017 1,869 1 View
this antibody trend attach to IgE
05 June 2017 2,476 0 View
hi dear friends. i run a simulation on my server. my server has 8 CPU core and 640 GPU core, but during of simulation don't used from 100 percent power of CPU core. how can i resolve it?
01 January 1970 2,643 2 View
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
07 August 2024 2,598 1 View
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View
If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...
28 July 2024 673 3 View
Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...
24 July 2024 367 4 View
I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...
19 July 2024 4,120 5 View
I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each...
17 July 2024 9,897 4 View
i am using the trjconv command in gromacs gmx_mpi -debug trjconv -s md.gro -f md.xtc -o utr.xtc -fit rot+trans and after few steps i got the error gmx_mpi': corrupted size vs. prev_size:...
17 July 2024 6,216 1 View
Hello everyone, This soudns like a strange question, but I created five XTC files using five different versions of GROMACS some years ago. All other files are missing, and I want to repeat the...
16 July 2024 7,205 2 View
Dear Gromacs users, I would like to simulate a zeolite-water system. In different literature, it is suggested to consider a rigid framework of zeolite to decrease the computational cost. I would...
15 July 2024 4,590 1 View
Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...
08 July 2024 4,724 4 View
