I have Gromacs 2019. when I want to run mdrun by GPU command I faced this error " Fatal error: Unexpected cudaStreamQuery failure: an illegal memory access was encountered. what is the problem and how I can solve it?
I couldn't find any detailed information about the way researchers find the exact thickness or distances of metal contacts in p-n junctions in articles or book. if you know any sources I'll be...
08 July 2024 7,546 1 View
hi, I have a PDB file of small molecules as chemical compounds (Figure 1) but I want to know their atom type like the PDB file of similar small molecules which has atom types such as CA, CB, ......
01 December 2023 229 5 View
Hi every one I have a peptide library (around 300 peptides) that I would like to dock peptides to its target while I want a high throughput molecular docking webserver or software to do this. Does...
07 October 2023 7,525 5 View
How can the valuable insights gained from these measurements be strategically applied to not only improve the sustainability of our environment but also elevate the effectiveness of urban...
25 September 2023 7,306 1 View
Hello everyone, I have a peptide library I want to filter my peptide library based on the stability and solubility of peptides. The Protparam webserver does not give a library of peptide files to...
24 September 2023 9,198 0 View
Hi everyone I want to model antibody structure but I do not have the sequence of the whole antibody. I just have the sequence of its CDR region. Do you know any web server to model antibody...
16 September 2023 6,806 2 View
Hello, I have performed NaCl extraction of a nuclear protein and run it on RP-HPLC with a mobile phase of acetonitrile in 0.1% TFA in water. I had repeatedly observed two tall peaks around minute...
13 April 2022 1,805 0 View
hello I want to make 2-dimensional plot like a picture as I attached I do not know how I can make it by gmx rms command in gromacs. could anyone help me with this issue?
23 October 2021 9,396 2 View
hello I want to measure free binding energy by gmx sham. but I do not know what is graph.xvg, gibbs.xvg and esham.xvg as input files in this command, and how I can generate...
23 October 2021 6,144 0 View
Hi everyone, I am just trying to do Gibson assembly using HiFi DNA Assembly Master Mix with 4 inserts and a double digested vector with BsaI and BbsI. The information about inserts is as below: 1....
18 October 2021 1,879 1 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 366 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 4,588 1 View
I want to reduce simulation time in CST for frequency domain solver by upgrading my computer. I already have discrete GPU but it doesn't seem to make any difference at all compared to integreted...
10 July 2024 2,789 4 View