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Hello all, I want to simulate Gamma amino acids using GROMACS, if anybody know where to get the forcefield parameters for gamma amino acids , kindly direct me .. Thanks in advance.
04 September 2021 8,616 5 View
2 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not...
31 August 2021 8,934 1 View
I am doing md simulation using gromacs. It showed that I have fatal error and according to the manual, the system is blowing up. However, Inhave increased the ns and decrease the fs but the...
30 August 2021 581 2 View
What is the best way of repeating simulations, say I have to run the 10 replicates of the same simulation trajectory which was previously simulated for 100 ns production run after minimization and...
30 August 2021 9,331 3 View
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 8,154 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 5,503 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 1,595 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 5,703 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 5,260 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 5,890 5 View
It is known that in order to quantify chaos in a dynamic system, the maximum Lyapunov exponent must be detected, but before applying Lyapunov detection, is there any way to know at a glance a...
16 August 2021 5,382 3 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 5,761 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 6,949 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 7,220 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 1,447 0 View
How to use gromacs to build topology after peptide C-terminal amidation ？
31 July 2021 135 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 6,718 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 4,835 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 3,311 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 1,829 2 View
I want to determine PNEWDT based on its value at the integration point previously. Can I define in a UMAT PNEWDT as : PNEWDT= min (PNEWDT, A) with A a specific variable calculated for each...
07 June 2021 5,556 0 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 6,705 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 7,843 0 View
We know about ths cosmic expansion, but what about the other kinematical invariants like shear and rotation? Concerning rotation there was a paper by Birch, but to my knowledge there were some...
16 April 2021 8,319 0 View