Re: [gmx-users] distance restraints between different chains

I think pulling code can solve the problem, http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#com-pulling On Fri, Mar 20, 2020 at 12:04 PM Oscar Hernandez Alba wrote: > Dear all, > > > > I am trying to run MD with a protein with four different chains. When > I >

[gmx-users] distance restraints between different chains

Dear all, I am trying to run MD with a protein with four different chains. When I convert this structure to gromacs, I have four different molecules in the topology file. I would like to use distance restraints between specific atoms of different chains. I have created the itp file with

[gmx-users] Distance restraints at topology file between gromacs-5.1.4 and gromacs-2018.4

Hi, Gromacs users and developers Actually, I used distance constraint for each chain.itp file. (for example, I added following for chainA.itp /chainB.itp/chainC.itp and so on [distance_restraints] ; i j ? label funct lo up1 up2 weight 155 1762

Re: [gmx-users] Distance restraints on two TYR OH groups so that they are together

I altered distance restraints according to your comment into: [ distance_restraints ]  195 281 1 1 1 0.4 0.44 0.48 1000Still get same issue that 195 and 281 even move away from each other. Here link to all files again, hopefully it will not be distorted.

Re: [gmx-users] Distance restraints on two TYR OH groups so that they are together

On 3/15/17 6:28 AM, Vytautas Rakeviius wrote: Hello, I try to add distance restraints on two TYR OH groups so that they are together in the end like this: [ distance_restraints ] 195 281 1 1 1 0.2 0.22 0.24 1000 But it does not work at least over time frame I tested, they even go further

[gmx-users] Distance restraints on two TYR OH groups so that they are together

Hello, I try to add distance restraints on two TYR OH groups so that they are together in the end like this: [ distance_restraints ]  195 281 1 1 1 0.2 0.22 0.24 1000 But it does not work at least over time frame I tested, they even go further away from each other. Here I share my all

Re: [gmx-users] distance restraints in mdp

Please don't reply to the entire digest. Copy the relevant portions and use a proper subject line. On 3/8/16 8:19 PM, Sana Saeed wrote: dear Justin Lemkuli already run that without restraints, it has no problems. even i used the gro file from the simple 5ns MD but still have these same errors

Re: [gmx-users] distance restraints in mdp

On 3/7/16 10:35 PM, Sana Saeed wrote: i am performing protein ligand binding free energy calculation MD. i have applied distance restraint to 1 pair of atoms. now when i am running md it gives me LINCS warnings. first i thought it is because of wrong geometry so i changed complex, now i am

[gmx-users] distance restraints in mdp

i am performing protein ligand binding free energy calculation MD. i have applied distance restraint to 1 pair of atoms. now when i am running md it gives me LINCS warnings. first i thought it is because of wrong geometry so i changed complex, now i am doing it for Lysozyme+JZ4. but still same

Re: [gmx-users] Distance Restraints

Dear Steve, First of all you should take a look in all mdp options regarding distance restraints: http://manual.gromacs.org/archive/4.5/online/mdp_opt.html#nmr I am not 100% familiar with dist res in version 4.5.4 but without dirse=simple for example I think you will not have any distance

[gmx-users] Distance Restraints

I have a two peptide system with  my second chain B having as part of its topology file (and sequence) a Zinc ion. That is, the Zinc ion is literally part of the chain so, that when I generate my itp files using pdb2gmx I get topol_proteinA.itp, topol_proteinB.itp (i.e. no topol_Ion.itp)...I

[gmx-users] Distance restraints

Dear All, I'm trying to keep distance restraints between few atoms, and for that I have done the following, In the topology file, I have inserted a block specifying the details of pairs -- ; Include forcefield

[gmx-users] Distance Restraints set for water-ion cluster in gas phase (vacuum)

Dear gromacs usres, I want to run nvt simulation of water-ion cluster (Na+(H2O)250) in gas phase (vacuum) at higher temperature ( bigger than 200 K). But the cluster will collapse at high temperature. So the distance restraints is used to restraint the water molecules and the ion Na+ not to

Re: [gmx-users] Distance Restraints set for water-ion cluster in gas phase (vacuum)

On 10/13/14 4:48 AM, liuyong_1...@dicp.ac.cn wrote: Dear gromacs usres, I want to run nvt simulation of water-ion cluster (Na+(H2O)250) in gas phase (vacuum) at higher temperature ( bigger than 200 K). But the cluster will collapse at high temperature. So the distance restraints is used to

Re: [gmx-users] Distance restraints does not work?

Thanks Justin. I was concerned about that the distance could increase so much above 0.4 (I had the feeling from the equation that the penalty was larger above up2(0.4)). 50.0000.4642269 100.0000.4505744 But anyway when I checked the interactions to Zn I found a competing