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Questions related to Gromacs
I have a question regarding Gromacs. I want to know whether Gromacs can calculate the interaction of each OH group of the sugar rings separately in bilayer or it just shows the number of whole HB...
27 August 2021 8,140 2 View
Hi all, Does gromacs have any option for adding external forces and torques to the atoms? the ones that change by the time and atom properties. like the fix add force and add torque command in...
26 August 2021 5,489 1 View
I've run a simulation for an apoprotein using fourierspacing = 0.16, and I want to run a protein-ligand complex simulation (all using Amber ff). I found that it's suggested to set the value of...
25 August 2021 1,582 5 View
I'm using Gromacs 2020 to run a protein ligand simulation using Amber99SB for protein and Amber (GAFF) for ligand, in the mdp files should rlist be of the same number as rcoulomb and rvdw e.g....
24 August 2021 5,690 2 View
I want to look at all my alanines in my protein chain and want a selection in VMD just for this. I don't know what their resID numbers are but want to be able to select them all by the fact they...
24 August 2021 5,250 1 View
Hi. I am running transmembrane protein simulation. I am confused at position restraining. During the shrinking steps using inflategro.pl script, tutorial mentions experimental value 0.69A but i do...
19 August 2021 5,878 5 View
Hello everyone, I want to use g_mmpbsa for interaction energy analysis Can anyone tell me about how can I install g_mmpbsa in gromacs 2020. Also, can anyone suggest me about which are the other...
07 August 2021 5,753 10 View
I've seen in some articles talked about parameterizing ions force field, for example here Effect of Ca2+ on the promiscuous target-protein binding of calmodulin the authors talked about...
05 August 2021 6,930 1 View
Is there any step-by-step protocol/procedure for the membrane protein (bilayer) ligand Gromacs Simulation? I could able to obtain a bilayer with the protein incorporated from the CHARMM GUI...
02 August 2021 7,207 2 View
I could able to obtain a bilayer with the protein incorporated from CHARM GUI sever, Now I am stuck; how to insert ligand on the system. I am looking forward to a useful site or protocol for this...
02 August 2021 1,439 0 View
How to use gromacs to build topology after peptide C-terminal amidation ?
31 July 2021 127 2 View
Hi, I would like to calculate the SASA of a protein structure. Along with the total SASA, it would be interesting to see the hydrophobic and hydrophilic surface area. I know there is a tool...
21 July 2021 6,707 5 View
Hello everybody, I am trying to download the top2psf.pl script from the VMD script library (https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/) but I am getting an error from...
20 July 2021 4,818 3 View
Hello all, I am new to MD and GROMACS. I was faced with the task of calculating the surface tension. As far as I know, the calculation parameters in *.mdp file, such as rvdw, rcoulomb, etc....
16 July 2021 3,301 3 View
Dear all, I'm in principle a NAMD user but I'm new in performing MD simulation using polarizable force field. I wonder if anyone can suggest any MD software (NAMD or GROMACS, or ..) to implement...
15 July 2021 1,814 2 View
(GROMACS) I have a multiple chain , while calculating rmsf , each chain is again starting from residue 1 but i wanted to get a continous graph ,so help me to get a continous rmsf graph or help me...
26 April 2021 6,694 2 View
The element based surface assembly__pickedsurf18 has a mixture of 3d shell edges and other types of underlying elements. If a surface has any 3d shell edges then all of its facets must be 3d shell...
19 April 2021 7,828 0 View
When I calculate the order parameter for lipid molecules I get positive value but many papers reports -SCH value. So is gromacs reporting -SCH values?
15 March 2021 731 8 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
04 March 2021 10,426 2 View
I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...
26 February 2021 6,760 1 View
I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.
19 February 2021 5,051 2 View
I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...
18 February 2021 1,335 3 View
Good day everyone! I am a Biochemistry undergraduate in the Philippines and to be very honest, we have no background in bioinformatics since we really focused on wet lab techniques + theory. Due...
16 February 2021 3,763 4 View
Dear All, I received a comment from reviewer about asking me selection of force field and water model. I choose OPLS-AAL and 3-point water model. They mentioned the combination of OPLS-AAL and SPC...
14 February 2021 1,583 3 View