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Questions related from Sotiris Papadatos
Hi all, I am performing a Molecular Dynamics simulation of a water pore inside a membrane. I am experimenting with some analysis options and I am having a bit of a trouble understanding the water...
02 February 2019 8,911 2 View
Hi, I am trying to calculate the distance between two atoms, which are defined in an index file. The command that I use is: "gmx distance -f output.gro -s prod.tpr -n index.ndx -oav...
08 August 2017 3,369 4 View
Hi, the default values for bonds, angles like kb, b0 etc, how are they calculated?
02 February 2017 5,349 2 View
Hi I am trying to simulate a protein containing a heme, using Gromacs and Charm27 force field. When I try to run pdb2gmx I get an error. I have looked the force field directory and found that this...
10 October 2016 3,027 2 View
Hi I want to perform an remd simulation of a large protein system. The bibliography I found so far is about small systems and doesn't describe the way they decide on the number of replicas or the...
08 August 2016 3,395 8 View
Hi, I am trying to simulate a protein using Replica Exchange. By reading at the literature I found what values are needed as a Tmin, Tmax and also the number of replicas. Apart from that there is...
08 August 2016 7,398 1 View
I am using Gromacs and I want to edit the ffbonded.itp in oplsaa.ff directory. I have by literature the bond length but I can't find the force constant. Is there a way to calculate it?
06 June 2015 1,898 5 View
I'm trying to add a molecule in aminoacids.rtp (new user) By looking at the pre defined amino acid entries and the chapter 5 of the manual I started building it up. The fields that the file...
05 May 2015 8,640 4 View
I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use.My problem is that I don't know how to continue, in theory I...
05 May 2015 5,458 3 View
