[gmx-users] reaction rate

Dear Gromacs users, I want to ask a question about reaction rate. As in umbrella sampling one can obtain Free energy profile of a reaction. Hence Ea- activation energy is known. To calculate the reaction rate one need to use Arrheniuss equation: K=Aexp(-Ea/RT). A - is a constant which characterize

[gmx-users] create a sphere of water molecules

Dear Gromacs Users, I want to add a sphere of water molecules around a ligand. I know I need to use -shell option in genbox. But first I I need to create a sphere. Please could you guide me? best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

[gmx-users] distorted structure

Dear gromacs users, I want to simulate small molecule - choline which is not neutral, it has uncompensated positive charge. When I transform mol2 file to pdb structure looks distorted (not correct) in VMD. I added with genion to the system a negative ions, but the pdb structure is still distorted.

[gmx-users] water residence time on a certain group of ligand

Dear gromacs users, I want to calculate water molecules residence time on a certain groups of a ligand. I found in gromacs exercises how to do it: https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html To get water residence time I need: 1) Obtain hbac.xvg, using this command: g_hbond -c

Re: [gmx-users] how many contacts has a certain atom at MD

. Lemkul > > > Olga Ivchenko wrote: > >> Yes, I want to plot number of contacts agains tempreture. But in >> thermodynamics when temperature changes the pressure changes or the volume. >> But in my system volume and pressure is the same at different tempretures. >>

Re: [gmx-users] Website search broken

I also have the same problem with the search. Olga 2011/2/23 Emine Deniz Tekin > Hi Justin, > > No matter what I search at gromacs search field, it gives the same error > message. > Deniz > > > On Wed, Feb 23, 2011 at 3:58 PM, Justin A. Lemkul wrote: > >> >> Hi, >> >> Is anyone else having pro

Re: [gmx-users] how many contacts has a certain atom at MD

same at different tempretures. best, Olga 2011/2/23 Justin A. Lemkul > > > Olga Ivchenko wrote: > >> If I am using g_mindist to calculate the number of contacts at different >> tempretures of the system. I am thinking if it will make sense because the >> system has

Re: [gmx-users] how many contacts has a certain atom at MD

which should be different at different tempretures is pressure. Please could you advice me on this? best, Olga 2011/2/21 Justin A. Lemkul > > > Olga Ivchenko wrote: > >> So I used mindist for a certain group of molecules which is surrounded by >> water. I got plot n

Re: [gmx-users] how many contacts has a certain atom at MD

if someone knows what is a creteria that a certain contact is formed? Is is a certain distance. best, Olga 2011/2/21 Olga Ivchenko > Thank you very much. > best, > Olga > > 2011/2/21 Justin A. Lemkul > > >> g_mindist -on (with suitable index groups) should al

Re: [gmx-users] how many contacts has a certain atom at MD

e moment. Version 4.0.x seem to work better. >> >> XAvier Periole skrev 2011-02-21 11.37: >> >>> g_dist >>> On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote: >>> >>> Dear Gromacs Users, >>>> >>>> I would like to know if th

[gmx-users] how many contacts has a certain atom at MD

Dear Gromacs Users, I would like to know if there is in gromacs an option how to calculate how many contacts has a certain atom i(n a molecules of interest) with water during the whole MD simulations (or at each step of MD). Please could you advice me on this? best, Olga -- gmx-users mailing lis

Re: [gmx-users] how to add hydrogen ions

Thank you for your reply. I am not planning to simulate proton transfer in gromacs. Just it could be nice to see possible interaction. best, Olga 2011/2/3 Erik Marklund > Mark Abraham skrev 2011-02-03 11.59: > > On 3/02/2011 9:18 PM, Olga Ivchenko wrote: >> >>> Dear

[gmx-users] how to add hydrogen ions

Dear Gromacs Users, I would like to replace some of my water molecules with H+ ions, or add hydrogen ions to my water box. Please could you advice me how to do it? Yours sincerely, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] proton proton exchange and constant pH simulations.

Just I heard that molecular mechanics proton proton transfer should be soon implemented in gromacs. That's why I am, asking it. 2011/1/27 Mark Abraham > On 27/01/2011 9:44 PM, Olga Ivchenko wrote: > >> Dear gromacs users, >> >> I want to ask if is it possible t

[gmx-users] proton proton exchange and constant pH simulations.

Dear gromacs users, I want to ask if is it possible to amke proton proton exchange simulations by now and constant pH simulations in new versions of Gromacs. best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

Re: [gmx-users] dipole moment

Thank you David, Olga 2011/1/25 David van der Spoel > On 2011-01-25 16.01, Olga Ivchenko wrote: > >> Dear David, >> >> I mean a dipole moment between a particle atom in a ligand and a >> particular atom in water molecule. G_dipoles works for molecules, as

Re: [gmx-users] dipole moment

Dear David, I mean a dipole moment between a particle atom in a ligand and a particular atom in water molecule. G_dipoles works for molecules, as I understood, not for atoms. best, Olga 2011/1/25 David van der Spoel > On 2011-01-25 14.51, Olga Ivchenko wrote: > >> Dear gromacs us

[gmx-users] dipole moment

Dear gromacs users, I would like to ask if there is a possibility in gromacs to calculate dipole moment between two atoms. For example one from water and another one from ligand. best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] g_rotacf NH vector relaxation

Dear gromacs users, I want to calculate NH vector for my ligand simulations using g_rotacf. I want to ask if I first need to remove rotation and translation degrees of freedom from the trajectory using the command: trjconv -f traj.xtc -s 10nsProd_MD.tpr -fit rot+trans -o no_rot_trans.xtc Also, wh

Re: [gmx-users] perl script for g_hbond

LIG1N1 LIG1O2 0.120 0.040 0.160 0.040 0.040 0.040 0.040 0.080 0.200 0.040 0.040 0.200 0.080 best, Olga 2010/11/29 Justin A. Lemkul > > > Olga Ivchenko wrote: > >> Hi Leila, >> >> I am also have a task to calculate

[gmx-users] -sel option for g_hbond

Dear Gromacs users, Does some one know if -sel option for g_hbond command is working in gromacs beta 4.5. Because when I try to run fir individual Hbonds privided in second index file gromacs can not recognize -sel command. Yours sincerely, Olga -- gmx-users mailing listgmx-users@gromacs.or

Re: [gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko)

sing cp-mcscf in l1003 > Level of SA at start = 0 > Segmentation fault > > Are you trying to use more than one thread? > > Gerrit > > Please could you advice me on this? > > 6. QMMM, Segmentation fault (Olga Ivchenko) >> >> >> > -- > gmx-user

[gmx-users] Re: QMMM, Segmentation fault

Dear gromacs users, > > I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2. > When I run DFT I got an error: > > number of CPUs for gaussian = 1 > memory for gaussian = 5000 > accuracy in l510 = 8 > NOT using cp-mcscf in l1003 > Level of SA at start = 0 > Segmentation fault

[gmx-users] QMMM, Segmentation fault

Dera gromacs users, I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2. When I run DFT I got an error: number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 Segmentation fault Please could you

Re: [gmx-users] proton proton transfer

Hi Erik, I think also I can try proton-proton transfer with gromacs later when it will be implemented. best, Olga 2010/12/2 Erik Marklund > Olga Ivchenko skrev 2010-12-02 13.30: > > Dear gromacs users, >> >> I want to simulate proton transfer between water and another

Re: [gmx-users] proton proton transfer

Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul > > > Olga Ivchenko wrote: > >> Dear gromacs users, >> >> I want to simulate proton transfer between water and another small >> molecule in gromacs. In the end I shoul

[gmx-users] proton proton transfer

Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there

Re: [gmx-users] perl script for g_hbond

Dear Justin, Thank you very much. best, Olga 2010/11/29 Justin A. Lemkul > > > Olga Ivchenko wrote: > >> Hi Leila, >> >> I am also have a task to calculate H-bonds frequency through the over all >> trajectory in gromacs. Please can you send me Jus

Re: [gmx-users] perl script for g_hbond

Hi Leila, I am also have a task to calculate H-bonds frequency through the over all trajectory in gromacs. Please can you send me Justin's script. If he does not mind. Yours sincerely, Olga 2010/11/29 leila karami > Dear Mark and gromacs users > > thanks for your time and consideration. > > yo

Re: [gmx-users] system is exploding

> > On 11/26/2010 11:26 AM, Olga Ivchenko wrote: > > Dear gromacs users, > > > > I am trying to run simulations for small molecules in water. Topology > files > > I created by my self for charm ff. When I am trying to start energy > > minimization I got an error

[gmx-users] system is exploding

Dear gromacs users, I am trying to run simulations for small molecules in water. Topology files I created by my self for charm ff. When I am trying to start energy minimization I got an error: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = 1000 That's means my system is

[gmx-users] (no subject)

Dear gromacs users, I want to heat system from 0K till 300K. Than do equilibration dynamics in water. I can not find any .mdp files where the system is gradually heated from initial temperature (0K) till needed temperature. I can only find NVP and NVT equilibration dynamics. Please can you advice

[gmx-users] Re: still can not run md for creatine

Hey Vitaly, Thank you for your reply. Here is the files: *itp:* ; ; ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; W

[gmx-users] still can not run md for creatine

Dear All, I still have troubles of starting running md for creatine. For which I created topology using PRODRG programm. The only difference between creatine.top and creating.itp is that creatine top has additional lines: #include "ffgmx.itp" #include "creatine.itp" Also please can you tell me w

Re: [gmx-users] Re: which force file has parameters for creatine md simulations?

sincerely, Olga 2010/11/10 Justin A. Lemkul > > > Olga Ivchenko wrote: > >> Dear All, >> >> I have created creating topology file using *prodrg_beta (using gromos 96 >> ff) <http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta>*. When I am >> tryi

[gmx-users] Re: which force file has parameters for creatine md simulations?

Dear All, I have created creating topology file using *prodrg_beta (using gromos 96 ff) *. When I am trying to run energy minimization it writes an error: Syntax error - File creatine.top, line 19 Last line read: '[ moleculetype ]' Invalid

[gmx-users] which force file has parameters for creatine md simulations?

Dear All, I want to do molecular dynamics with creatine. But I can not transform creatine pdb file downloaded from drugbank to gromac topology file using command: pdb2gmx -f Please can you write me if there is a force filed for which creatine parameters are already exist and I can use this forcef

[gmx-users] which force file has parameters for creatine md simulations?

Dear All, I want to do molecular dynamics with creatine. But I can not transform creatine pdb file downloaded from drugbank to gromac topology file using command: pdb2gmx -f Please can you write me if there is a force filed for which creatine parameters are already exist and I can use this forcef

[gmx-users] which force file has parameters for creatine md simulations

Dear All, I want to do molecular dynamics with creatine. But I can not transform creatine pdb file downloaded from drugbank to gromac topology file using command: pdb2gmx -f Please can you write me if there is a force filed for which creatine parameters are already exist and I can use this forcef