Re: [gmx-users] Pulling two groups in opposite direction

> > On 5/16/18 3:32 AM, Naba wrote: > > Dear all, > > > > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino > > acids from its homodimer in opposite directions along z axis. The > > interfaces of each protein chain is parallel to the z axis. I do not need > > any restraints in

[gmx-users] Protein protein complex simulation to be done with respect to observe changes in temperature

Dear all, Do we need to change any other parameters other than ref_t and gen_temp should be changed if I want to perform protein protein complex md simulation at different temperatures of the same input protein. Is it necessary to equilibrate the average pressure value to 1 bar before running the

[gmx-users] partial exclusion of interactions within 1-4

Hi all, I think I understand how it works, but to double-check... There's a paper describing a setup of intramolecular interactions for boron nitride ( https://pubs.acs.org/doi/10.1021/acs.jpclett.7b03443), in which non-bonded interactions *within* 1-4 were set up in the following way: LJ is off,

Re: [gmx-users] Pulling two groups in opposite direction

On 5/16/18 3:32 AM, Naba wrote: Dear all, I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino acids from its homodimer in opposite directions along z axis. The interfaces of each protein chain is parallel to the z axis. I do not need any restraints in this case. I have gone

Re: [gmx-users] C6-C12 table potential

Hi, Thanks. On Wed, May 16, 2018 at 3:09 PM, Mark Abraham wrote: > Hi, > > I would assume not, because it's more useful to be able to let a user > specify a table for an energy group and for that to contain different atom > types. > I'm afraid I did get your point!

Re: [gmx-users] C6-C12 table potential

Hi, I would assume not, because it's more useful to be able to let a user specify a table for an energy group and for that to contain different atom types. But your best friend is to test both your understanding and the code by e.g. making a structure file with two such atoms 1nm apart and

[gmx-users] C6-C12 table potential

Hi, Suppose that the C6 and C12 for the nonbonded interaction between two beads of P4 and SNa in the Martini force fields are as following: C6 C12 P4SNda1 0.17246E-00 0.18590E-02 ; semi attractive Now, I was wondering how I

[gmx-users] Topology file

Dear all, I want to create a topol.top file for Silica slab for which the force fields parameters are available in literature as well as in the lammps.data file which works fine in lammps (below links). The slab has in general 2184 atom including two types of O atom(OS in surface part and OB in

Re: [gmx-users] secondary structure analysis

You may want to familiarize yourself with how the terminal works before proceeding. You need to give the path on your machine for dssp. On Wed, May 16, 2018 at 12:13 PM, SHAHEE ISLAM wrote: > when i am using command > dssp -h > below are shown on the terminal screen >

Re: [gmx-users] secondary structure analysis

when i am using command dssp -h below are shown on the terminal screen DSSP 2.0.4 options: -h [ --help ] Display help message -i [ --input ] argInput file -o [ --output ] arg Output file, use 'stdout' to output to screen -v [ --verbose ] Verbose output --version

Re: [gmx-users] Regarding MD simulations involving metal ion (Mn)

Hello, for metal ions (and especially transition metals) you should first consider what kind of metal model you want to employ, as the different models (bonded, soft sphere or dummy model) have have different properties. There are numerous papers outlining the parametrization of those

Re: [gmx-users] secondary structure analysis

Have you tried running the dssp command on a pdb file to ensure that it is working as intended? FYI 4.5.5 is no longer supported so you may want to consider upgrading to (the much faster) gromacs 2018. On Wed, May 16, 2018 at 11:45 AM, SHAHEE ISLAM wrote: > i have

[gmx-users] Regarding MD simulations involving metal ion (Mn)

Dear All, I need to simulation of protein-ligand with coordinated metal ion bound to ligand. The metal ion is Mn+2, Advise me whether its correct to use CHARMM36 and OPLSS force field for parameterization? What things should taken care while simulating such cases where we have metals with

Re: [gmx-users] secondary structure analysis

i have installed dssp2.04 in usr/local/bin. On 5/16/18, Joe Jordan wrote: > You have to point to where you have dssp installed. This may require you to > install dssp. > > On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM > wrote: > >> i want calculate

Re: [gmx-users] secondary structure analysis

You have to point to where you have dssp installed. This may require you to install dssp. On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM wrote: > i want calculate the secondary structure of protein in gromacs.but > when i am using this command > > do_dssp -f dynamic.xtc

[gmx-users] secondary structure analysis

i want calculate the secondary structure of protein in gromacs.but when i am using this command do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10 getting this error Program do_dssp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: 572

[gmx-users] Pulling two groups in opposite direction

Dear all, I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino acids from its homodimer in opposite directions along z axis. The interfaces of each protein chain is parallel to the z axis. I do not need any restraints in this case. I have gone through the GROMACS manual and some