[gmx-users] Segmentation fault and PCA Analysis

Dear users, I am trying to align my trajectory to an average structure pdb, the problem is that I have "Segmentation fault (core dumped)" while taking this pdb as a reference structure, while it worked with the em.tpr file ... I also tried to extract the pdb from the that em.tpr using gmx

[gmx-users] Rerun

Dear users, Will the .trr files produced from rerun of .xtc files be the same if it was produced during the original MD simulation? Kind regards,Ahmed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] rerun

Dear users, Will the .trr file produced from rerun of .xtc files the same if it was produced during the original MD simulation? Kind regards,Ahmed  -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] RMSD values consideration

Try using trjconv to remove pbc before analysis Regards,Ahmed On Wed, 28 Mar, 2018 at 8:43 am, SHYANTANI MAITI wrote: Dear all, After using this command for computation of rmsd of backbone of protein protein complex consisting of three proteins :

Re: [gmx-users] rvdw and rcoulomb

cs.org Sent: Tuesday, March 13, 2018 12:18 PM Subject: Re: [gmx-users] rvdw and rcoulomb On 3/13/18 5:17 AM, Ahmed Mashaly wrote: > Thanks guys > > It is AMBER ff > Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 > for continuation with no effect on the

Re: [gmx-users] rvdw and rcoulomb

l.szil...@gmail.com> wrote: >Note that rcoulomb, unlike rvdw, when using a PME long-range >electrostatics, is tunable (together with the PME grid spacing). >-- >Szilárd > > >On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>

[gmx-users] rvdw and rcoulomb

Dear users, Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed -- 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 http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] NVT NPT restrains

ary 20, 2018 7:55 PM Subject: Re: [gmx-users] NVT NPT restrains On 2/20/18 1:47 PM, Ahmed Mashaly wrote: > Hi > > About the restrains, I see that it is necessary for NVT and NPT. > For the .top and .gro produced by Acpype, > https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDj

[gmx-users] NVT NPT restrains

Hi About the restrains, I see that it is necessary for NVT and NPT. For the .top and .gro produced by Acpype, https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM I don't have porse.itp nor anything related to restrain in the .top file, only for water #ifdef FLEXIBLE [ bonds ] ;

[gmx-users] Energygrps

Hi What is the default engerygrps to be written if I don't specify them in the mdp file? And if I have more than one ligand and want to calculate the energy between them and the protein, and also between one part of the protein (loop) and the rest of the protein I should make an index

Re: [gmx-users] simulated annealing

ed annealing On 2/19/18 2:31 PM, Ahmed Mashaly wrote: > Thanks, Justin. > > I had set it to 300K before (as the original mdp was), but now I found others > with 0 > > > Now when if we look at the log file, you can see ref temp for both groups > starts from 0

[gmx-users] simulated annealing

Hi If I want to heat the system from 0 to 300K gradually in NVT via simulated annealing the ref-t and gen-temp should be 0 or 300?  Kind Regards,Ahmed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] PBC

Hi If I want to use gmx trjconv to recenter the protein in xtc file, the reference (-s) .tpr should be the one I used in simulation (md.tpr) or I can use the first one (em.tpr) without a difference? This is because the protein has jumped after em step, and if I have to use md.tpr as reference

[gmx-users] RMS for many trajectories

Hi Is there a way to calculate rms for 20 trajectories without joining them? Kind Regards,Ahmed -- 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] Running long MD simulation

Sorry, I see the point of ndx now ... I thought there was no default group for water_and_ions. However, the second question is still running through my head Kind Regards,Ahmed  From: Ahmed Mashaly <mashaly_1...@yahoo.com> To: "gmx-us...@gromacs.org" <gmx-us...@

Re: [gmx-users] Running long MD simulation

and SOL the same!  Kind Regards,Ahmed Mashaly From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Sunday, February 4, 2018 4:02 PM Subject: Re: [gmx-users] Running long MD simulation On 2/4/18 9:57 AM, Ahmed Mashaly wrote: > And the index file? what is

[gmx-users] Octahedral minimization problem

Hi Two solvated systems with amber were converted to .gro with acpype. one is box the other is octahedral The box can be minimized in cluster with this em.mdp file integrator = steep emtol = 100.0 emstep = 0.01 nsteps = 5 nstlist = 1 cutoff-scheme ns_type = grid coulombtype = PME

Re: [gmx-users] Running long MD simulation

ct: Re: [gmx-users] Running long MD simulation On 2/4/18 9:15 AM, Ahmed Mashaly wrote: > Thanks Justin. > > I found this one: > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118282.html > > Another question I have about using cpt > >

Re: [gmx-users] Running long MD simulation

From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Friday, February 2, 2018 5:27 PM Subject: Re: [gmx-users] Running long MD simulation On 2/1/18 12:45 PM, Ahmed Mashaly wrote: > Hi > I want to run a long MD 200 ns, but I want

[gmx-users] Running long MD simulation

Hi I want to run a long MD 200 ns, but I want the outputs of every 5 ns to be saved separately ... Is there a way or a script to do this? Kind Regards,Ahmed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] Grompp warning about topology constrains

Thanks Justin Kind Regards,Ahmed Mashaly From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Tuesday, January 30, 2018 6:00 PM Subject: Re: [gmx-users] Grompp warning about topology constrains On 1/30/18 5:46 AM, Ahmed Mashaly wrote: > > T

Re: [gmx-users] Grompp warning about topology constrains

edu> To: gmx-us...@gromacs.org Sent: Tuesday, January 30, 2018 2:14 AM Subject: Re: [gmx-users] Grompp warning about topology constrains On 1/29/18 11:03 AM, Ahmed Mashaly wrote: > Hi, > I have set up my parameters with tleap, converted to gromacs with Acpype, did > the minimization

[gmx-users] emtol value

Hi, What should be the emtol value for big proteins and system? speaking about +1500 residue and +50k water molecule.  -- 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

[gmx-users] Grompp warning about topology constrains

Hi, I have set up my parameters with tleap, converted to gromacs with Acpype, did the minimization. For NVT, when I use grompp, this warning appears: WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of an angle, connected by constraints and  with masses that differ by

[gmx-users] Recentering a protein

Hi I am new to gromacs (using v. 2016.4) and need to check the following steps for my system. 01. I have prepared the system with Amber 14, minimized, heated to 300K, equilibrated 02. Then I used Acpype to convert the amber top and equilibrated  rst file to gromacs .top and .gro files03.