[gmx-users] distance restraint in gromacs md run

Hi, I have a protein of interest which requires distance restraint for C alpha atoms. However, the simulation does not seem to include the restraint at all. *prod.mdp* define = -DPOSRES constraints = none integrator = md dt = 0.005 nsteps

[gmx-users] Pulling in opposite directions

Dear users, I would like to perform an umbrella sampling by pulling two metal ions (two pull groups) away from protein (reference group) in opposite directions. I could restrain the positions of protein atoms (reference group) and then perform the pulling simulation. But how do I ensure that one

[gmx-users] hydrogen bond analysis

Dear all For hydrogen bond analysis, we generate *.xvg file for -num tag in gmx hbond command. My inquiry is in the xvg file there are three column output. First column is time. Which one is hydrogen bond number? If number 2 column is hydrogen bond number in every frame than what is number 3

Re: [gmx-users] Insert Gold nanoparticles in a simulation box

Simply copy/paste the text from the coordinate file for the nano particle onto the end of the coordinate file for the monolayer. Of course, you need to only insert the coordinate lines, not the text at the start (description and number of atoms in a .gro file) or end (box dimensions in a .gro

[gmx-users] error in phosphoserine simulation during MD

thank you very much I tried to complete pdb file, but since pdb file containing phosphoserine which is different from its sequence, because there is serine in its sequence file, when I wanted to use modeller, I confronted these error " sequence difference between alignment and pdb. I used

Re: [gmx-users] How to parameterize the volume occupied by a protein?

Hi Mark, I decided to write my own script, which computes distances between silica and protein atoms as you suggested. Removing the silica is not trivial because one must remove SiO2 molecules but there is no unique way to partition a silica block into SiO2 molecules. .Jose On Fri, Jun 16, 2017

Re: [gmx-users] error in phosphoserine simulation during MD

On 6/18/17 2:19 PM, marzieh dehghan wrote: Hi Dear Justin Thanks a lot for your kind answer, I applied two types of command to get rid of the previous error *at first*, the following command was used: *gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc * but I confronted these

[gmx-users] error in phosphoserine simulation during MD

Hi Dear Justin Thanks a lot for your kind answer, I applied two types of command to get rid of the previous error *at first*, the following command was used: *gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc * but I confronted these error CYS901 SG7090 1.414 CYS905 SG7117

Re: [gmx-users] CompEL bulk offset parameter unavailable in gromacs 5.1.4?

> On 18. Jun 2017, at 13:40, Vries, de, H.W. > wrote: > > dear all, > > I am employing the computational electrophysiology scheme in gromacs 5.1.4. > I want to set a bulk-offset parameter, such that the scheme only does > position exchanges in a region that is

[gmx-users] CompEL bulk offset parameter unavailable in gromacs 5.1.4?

dear all, I am employing the computational electrophysiology scheme in gromacs 5.1.4. I want to set a bulk-offset parameter, such that the scheme only does position exchanges in a region that is remotely enough from my protein. However, it seems that I am not able to set the 'bulk-offset'