Re: [gmx-users] .coordinate(gro) file

Fitsiou already suggested you to change the number of atoms at top second line of the gro file. On Mon, Nov 6, 2017 at 10:22 AM, rose rahmani wrote: > Hi dear > > yes,i did > > On Mon, Nov 6, 2017 at 12:07 AM, Fitsiou, Eleni > > wrote: > > >

[gmx-users] angle/distance/position restraints in alchemical free energy calculation

I want to apply distance or angle restraints between any atoms of protein and any atoms of ligand to maintain the initial binding mode of ligand in the protein when non-bonded interactions entirely turned off. As described in figure 1 from the article (http

Re: [gmx-users] Determining a ligands permeability

Hi, Justin, Thanks for your question. Presume that ligands were in only one side of the box outside of the membrane. 1)In metadynamics, the membrane will be pushed by the ligands. After long time simulation, the membrane may move along the Z-axis. 2)In steer MD, one ligand will be pulled

[gmx-users] water molecule cannot be settled during minimization!!!!

Dear gromacs users I am trying to simulate one protein with 180 residues. During energy minimization I got the falling error. Fatal error: step 26: Water molecule starting at atom 28787 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I have reduced the em

Re: [gmx-users] .coordinate(gro) file

Hi dear yes,i did On Mon, Nov 6, 2017 at 12:07 AM, Fitsiou, Eleni wrote: > Hi, did you change the total number of atoms in your file ? > (the second line at the top of the gro file?) > > Best, Eleni > > On 5 Nov 2017, at 20:33, rose rahmani

Re: [gmx-users] angle/distance/position restraints in alchemical free energy calculation

On 11/5/17 8:35 PM, minky son wrote: I want to do it using gromacs. Is there any way to control those restraints (except dihedral angle) in gromacs? You can set up any sort of bonded interactions (all of which can be perturbed via the free energy code) using an

[gmx-users] angle/distance/position restraints in alchemical free energy calculation

I want to do it using gromacs. Is there any way to control those restraints (except dihedral angle) in gromacs? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] pdb (CTAB) into .GRO

Justin is right, x2top is not "smart" but it can get you in the point you in a helpful direction. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics

Re: [gmx-users] osmolytes box generation in gromacs

It's just a simple chemistry calculation that you will have learned in secondary school chemistry: n(glycine) = [glycine] * Vol(box) Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC

Re: [gmx-users] .coordinate(gro) file

Hi, did you change the total number of atoms in your file ? (the second line at the top of the gro file?) Best, Eleni > On 5 Nov 2017, at 20:33, rose rahmani wrote: > > Hi > > I have structure.gro file > > 32 > . > . > . > > 0ZnSS29 29 0.000 0.191 2.029

[gmx-users] .coordinate(gro) file

Hi I have structure.gro file 32 . . . 0ZnSS29 29 0.000 0.191 2.029 0ZnSS30 30 0.000 0.574 2.029 0ZnS Zn31 31 0.000 0.000 2.164 0ZnS Zn32 32 0.000 0.383 2.164 0.0 0.0 0.0 and AA.gro PRODRG COORDS 12 1PDB O

[gmx-users] .coordinate(gro) file

Hi I have structure.gro file 32 . . . 0ZnSS29 29 0.000 0.191 2.029 0ZnSS30 30 0.000 0.574 2.029 0ZnS Zn31 31 0.000 0.000 2.164 0ZnS Zn32 32 0.000 0.383 2.164 0.0 0.0 0.0 and AA.gro PRODRG COORDS 12 1PDB O

Re: [gmx-users] converting .xtc into .xyz

> On Nov 5, 2017, at 10:13 AM, Justin Lemkul wrote: > > On 11/4/17 3:22 PM, Iman Ahmadabadi wrote: >> Dear Users, >> >> How could I convert .xtc (or .trr) file of output of a run frames into .xyz >> format? my mean is to obtaining one .xyz file for whole frames that created >>

Re: [gmx-users] Determining a ligands permeability

On 11/5/17 7:40 AM, Du, Yu wrote: Hi, I don't study the membrane permeability of small molecules and can't give related papers. All in all, you need to first successfully simulate the lipid-small molecule system and then enhanced sampling because of the time scale of ligand diffusing

Re: [gmx-users] converting .xtc into .xyz

On 11/4/17 3:22 PM, Iman Ahmadabadi wrote: Dear Users, How could I convert .xtc (or .trr) file of output of a run frames into .xyz format? my mean is to obtaining one .xyz file for whole frames that created by run? Use trjconv to convert to a plain-text trajectory format like .gro or .pdb

Re: [gmx-users] pdb (CTAB) into .GRO

On 11/3/17 10:38 AM, Smith, Micholas D. wrote: One thing to try is to build the CTAB molecule with gmx x2top. You'll need to be careful about what it produces, but it can be helpful. The only word of caution here is that you have to still tell x2top what everything's charges and

Re: [gmx-users] force field / parameters for NADH, FMN

On 11/3/17 10:33 AM, Hermann, Johannes wrote: Hey Justin, thanks - again -  for your reply! Now I get duplicated parameters warnings and errors: WARNING 1 [file fmn.prm, line 5]:   Overriding Bond parameters.   old:  0.1295 405848 0.1295 405848  

Re: [gmx-users] dipole on an atom

On 05/11/17 16:07, Faezeh Pousaneh wrote: Yes, exactly. But my atom is uncharged sphere, I'll bring two similar size and similar mass (+ -) ions inside the sphere. So rotation will not happen then for atom. If you simulate multiple such spheres they will behave like a Stockmayer dipolar

[gmx-users] Dynamic Load Balancing Crash

Hello, I recently started experiencing a error with GROMACS 2016.3 during a replica exchange simulation with 80 replicas, 480 cpus, and 40 GPUs: Assertion failed: Condition: comm->cycl_n[ddCyclStep] > 0 When we turned on DLB, we should have measured cycles The simulation then crashes. I turned

Re: [gmx-users] dipole on an atom

Yes, exactly. But my atom is uncharged sphere, I'll bring two similar size and similar mass (+ -) ions inside the sphere. So rotation will not happen then for atom. On Nov 5, 2017 16:00, "David van der Spoel" wrote: On 05/11/17 15:54, Faezeh Pousaneh wrote: > So I guess

Re: [gmx-users] dipole on an atom

On 05/11/17 15:54, Faezeh Pousaneh wrote: So I guess the only solution can be: I take two small ions bring them inside original atom, parametrize their interactions with each other and the initial atom such that they stick inside the atom. What do you think? In fact you are then creating a

Re: [gmx-users] dipole on an atom

So I guess the only solution can be: I take two small ions bring them inside original atom, parametrize their interactions with each other and the initial atom such that they stick inside the atom. What do you think? Best regards On Sun, Nov 5, 2017 at 3:42 PM, David van der Spoel

Re: [gmx-users] dipole on an atom

On 04/11/17 19:19, Faezeh Pousaneh wrote: Hi, I have an uncharged atom, and I would like to give it a dipole. Any suggestion? impossible in gromacs. Best regards -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596,

Re: [gmx-users] Determining a ligands permeability

Hi, I don't study the membrane permeability of small molecules and can't give related papers. All in all, you need to first successfully simulate the lipid-small molecule system and then enhanced sampling because of the time scale of ligand diffusing across the membrane. There are some

[gmx-users] Determining a ligands permeability

I have tried to do an umbrella sampling for a ligand (drug) and membrane as per the gromacs tutorial. Now i want to calculate permeability and diffusibility for this ligand, so can anyone suggest how to proceed further. Since there is some literature available but it does not show the proper