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
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
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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
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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 :
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
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:
>>
>>
>>
Dear users,
Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed
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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
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 ]
;
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
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
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
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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
Hi
Is there a way to calculate rms for 20 trajectories without joining them? Kind
Regards,Ahmed
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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...@
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
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
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
>
>
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
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
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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
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
Hi,
What should be the emtol value for big proteins and system? speaking about
+1500 residue and +50k water molecule.
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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
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.
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