Re: [gmx-users] query regarding state.cpt file

Dear Dr. Justin, Thank you so much for the reply. Regards ~ Sudha On Thu, Jan 17, 2019 at 3:41 AM Justin Lemkul wrote: > > > On 1/15/19 11:29 PM, sudha bhagwati wrote: > > MD_output.tar.gz > > < > https://drive.google.com/file/d/1aJewpvBzeeH4C6o53nCl2qaPTCFDaDeD/view?usp=drive_web > > > >

Re: [gmx-users] Doubt about Steered molecular dynamics

Hi Justin, What if I use the reference group is the absolute position in space by specifying pull-coord1-origin: x0 y0 z0? How about the force on this point now? Thanks On Thu, Jan 17, 2019 at 12:24 AM Justin Lemkul wrote: > > > On 1/16/19 6:22 PM, Quyen Vu Van wrote: > > Hi Everyone, > >

Re: [gmx-users] Doubt about Steered molecular dynamics

Sorry Justin, Could you please explain in more details? Thanks On Thu, Jan 17, 2019 at 12:24 AM Justin Lemkul wrote: > > > On 1/16/19 6:22 PM, Quyen Vu Van wrote: > > Hi Everyone, > > Please help me to understand about COM Pulling in gromacs? > > As I understand from Justin's tutorial, a dummy

Re: [gmx-users] Doubt about Steered molecular dynamics

On 1/16/19 6:22 PM, Quyen Vu Van wrote: Hi Everyone, Please help me to understand about COM Pulling in gromacs? As I understand from Justin's tutorial, a dummy atom will be attached to the center of mass of Protein A through a spring with a force constant of 1000kJ / mol / nm ^ 2

[gmx-users] Doubt about Steered molecular dynamics

Hi Everyone, Please help me to understand about COM Pulling in gromacs? As I understand from Justin's tutorial, a dummy atom will be attached to the center of mass of Protein A through a spring with a force constant of 1000kJ / mol / nm ^ 2 (pull_coord1_k) and pulling along the positive direction

Re: [gmx-users] query regarding state.cpt file

On 1/15/19 11:29 PM, sudha bhagwati wrote: MD_output.tar.gz Greetings Sir/Madam I am running MD simulation using commands listed below-

Re: [gmx-users] core dumped

On 1/15/19 12:58 PM, rabee khorram wrote: Hello; Thank you Justin for your answer. I have mailed fe2o3.pdb file in this gmail for you. The mailing list does not accept attachments, nor would a PDB file be useful here. in atomname2type.n2t, for Fe-O bonds, I have used Fe type From

Re: [gmx-users] No pressure coupling in X direction

On 1/16/19 4:04 PM, Sam David wrote: Hi I have no idea about pull code but if you want pressure in a specific direction you can use anisotropic coupling where it has xx yy zz xy xz yz in your case xx=0, yy=p zz=p xy=xz=yz=0 Anisotropic pressure coupling can lead to distortion of the unit

Re: [gmx-users] No pressure coupling in X direction

Dear Sam, Thanks for your help. Best Virus-free. www.avast.com

Re: [gmx-users] No pressure coupling in X direction

Hi I have no idea about pull code but if you want pressure in a specific direction you can use anisotropic coupling where it has xx yy zz xy xz yz in your case xx=0, yy=p zz=p xy=xz=yz=0 check it online Best On Wed, Jan 16, 2019 at 1:50 PM Quyen Vu Van wrote: > Dear all, > In pull code, I

[gmx-users] No pressure coupling in X direction

Dear all, In pull code, I want to use *pull-coord1-geometry=direction-periodic* and Gromacs requires no pressure coupling in the pulling direction, which is x-direction in my case. How can I just use pressure coupling for y-z direction? Best regards, Quyen -- Gromacs Users mailing list * Please

[gmx-users] COM pulling: Reference position in space

Dear GMX community, I read on manual of gromacs that the reference group in pulling code can be defined by absolute position in space. How can I change my setup for that purpose, for example the coordinate of reference point X0 Y0 Z0 ; Pull code pull= yes pull_ncoords

Re: [gmx-users] Use all-atom PDB or coarse-grained PDB as the restraints for grompp a coarse-grained gro?

Sorry for asking this. I now understand it. See post at https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/123809.html -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Wed, Jan 16, 2019 04:27 AM To:

Re: [gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?

Hi Mark, Thank you for your help! Sorry I was totally confused. I thought I should delete the "define = -DPOSRES" option and use "-r target.pdb". Now I understand that. I should ) still keep the "define = -DPOSRES" in the mdp file ) still keep the "[ position_restraints ]" section in the itp

Re: [gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?

Hi, Nothing has changed in the implementation. Atoms which have interactions specified have always had get position coordinates to target from somewhere. (Those atoms with no position restraint interactions never cared.) Historically the position coordinates came from the file you used for -c if

[gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?

My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to replace the "define = -DPOSRES" option in the .mdp file. However, how can I do position restraints only for certain atoms, e.g. only the backbone atoms? I think, if I use "-r target.pdb", both the backbone and side chain

Re: [gmx-users] GROMACS Infrastructure

Hi Nam Pho, > On 16. Jan 2019, at 01:40, Nam Pho wrote: > > Hello GROMACS Users, > > My name is Nam and I support a campus supercomputer for which one of the > major applications is GROMACS. I was curious if anyone has optimized > servers for cost and has a blueprint for that, yes, we did! We