On 12/2/19 10:06 AM, Ayesha Fatima wrote:
Dear All,
Good morning. I am doing the Protein Ligand complex simulation tutorial
from the Gromacs website. I followed the tutorial without any issue. When I
want to run the energy minimisation md, i get the error message
Are you working through the
This is due to the bad initial structure.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
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Dear All,
Good morning. I am doing the Protein Ligand complex simulation tutorial
from the Gromacs website. I followed the tutorial without any issue. When I
want to run the energy minimisation md, i get the error message
Fatal error:
grid cell cx -2147483648 cy -2147483648 out of range (max 24 2
us...@gromacs.org
> Subject: [gmx-users] ENERGY MINIMISATION
> To: gromacs.org_gmx-users@maillist.sys.kth.se
>
> > Dear gromacs family members,
> > I am doing energy minimisation of a 250 molecule acetamide
> system
> > in gromacs 2018.3. The energy minimi
-
Date: Thu, 6 Jun 2019 11:23:36 +0530
From: Dhrubajyoti Maji
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] ENERGY MINIMISATION
To: gromacs.org_gmx-users@maillist.sys.kth.se
Dear gromacs family members,
I am doing energy minimisation of a 250 molecule acetamide system
in
.gro files do not contain any information about bonds, only the coordinate
of each atom/particle. VMD guesses which atoms are bonded together based on
their separation.
On Thu, 6 Jun. 2019, 3:53 pm Dhrubajyoti Maji, wrote:
> Dear gromacs family members,
> I am doing energy minimisation
Dear gromacs family members,
I am doing energy minimisation of a 250 molecule acetamide system
in gromacs 2018.3. The energy minimisation process runs smoothly without
any warning. But when I see the resultant gro file through VMD I find
several bonds are broken. Please suggest about this
Hi,
Please read the advice on system preparation on the GROMACS webpage. You
probably have clashing atoms or missing atoms (check all the warnings!)
Mark
On Tue, 6 Jun 2017 20:19 Pandya, Akash wrote:
> Hi all,
>
> I have used the steepest descent method to minimise my system. It kept
> saying
Hi all,
I have used the steepest descent method to minimise my system. It kept saying
certain water molecules could not be settled but it still managed to reached
the maximum force. Then I used the Conjugate gradient method and I get this
error message. Can someday please tell me how I would ch
That’s a good suggestion, Mark. Will do :-)
Thanks
Anthony
Dr Anthony Nash
Department of Chemistry
University College London
Skeletal Tissue Dynamics Group
Committee member of London Matrix Group @LondonMatrixGrp
On 03/10/2016 12:03, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
beh
Hi,
Sounds like you could check the output from that tool, and if it gave no
warning (or offers you no way to choose another rotamer) then you could
make some constructive feedback to its authors :-)
Mark
On Mon, 3 Oct 2016 11:22 Nash, Anthony wrote:
>
> Hi Justin,
>
>
> I’ve tried out all of
Hi Justin,
I’ve tried out all of your suggestions, they worked to an extent but the
in vacu idea was a good call as it’s actually helped me isolate what the
real problem is: I-TASSER has put the C-N backbone bond of two residues
through the ring of an adjacent PHE residue!
Thanks
Anthony
On
Please don't reply to digests or unrelated threads when starting a new topic; it
creates a mess in the archive.
On 10/2/16 6:11 PM, Nash, Anthony wrote:
Hi all,
I had a homology/de-novo model .pdb converted into .gro, solvated,
neutralised and now I¹m going through a series of energy minimis
Hi all,
I had a homology/de-novo model .pdb converted into .gro, solvated,
neutralised and now I¹m going through a series of energy minimisation
steps. Unfortunately, during energy minimisation I get LINCS WARNINGS
(angle relative constraint deviation). The the naked eye, the atoms
involved don¹t
at 07:54, <
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se> <
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
> >
> > From: Justin Lemkul mailto:jalem...@vt.edu>>
> > Subject: Re: [gmx-users] Energy minimisation goes to several values
> >
be turned on during energy minimization or just started from heating?
Thanks in advance,
Kevin
> On 27 Jun, 2015, at 07:54,
>
> wrote:
>
> From: Justin Lemkul mailto:jalem...@vt.edu>>
> Subject: Re: [gmx-users] Energy minimisation goes to several values
> Date:
22:21, mailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se>>
mailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se>> wrote:
*From:*Justin Lemkul mailto:jalem...@vt.edu>>
*Subject:**Re: [gmx-users] Energy minimisation goes to several values*
*Date:*26 June, 2015 21:27:32 HKT
longer calculation time in total or it will
give a bad final structure?
Thanks in advance,
Kevin
> On 26 Jun, 2015, at 22:21,
>
> wrote:
>
> From: Justin Lemkul mailto:jalem...@vt.edu>>
> Subject: Re: [gmx-users] Energy minimisation goes to several values
> Date:
On 6/25/15 9:45 PM, Kevin C Chan wrote:
Dear Users,
I am energy minimising a quite large solvated system containing protein and
lipids (~800,000 atoms). I used to fix components of the system in order to
speed-up energy minimisation and sometimes it is easier to debug such
processes. Here is m
Dear Users,
I am energy minimising a quite large solvated system containing protein and
lipids (~800,000 atoms). I used to fix components of the system in order to
speed-up energy minimisation and sometimes it is easier to debug such
processes. Here is my protocol:
1. fix all except water and so t
On 6/12/14, 7:14 AM, Balasubramanian Suriyanarayanan wrote:
But is not "confout.gro" the output of the compression step.
the command is
"perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat"
or else what is the output of above command.
Read the InflateGRO documentation (to
But is not "confout.gro" the output of the compression step.
the command is
"perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat"
or else what is the output of above command.
regards
suriyanarayanan
On Thu, Jun 12, 2014 at 3:13 PM, Justin Lemkul wrote:
>
>
> On 6/12/14,
On 6/12/14, 4:54 AM, Balasubramanian Suriyanarayanan wrote:
Dear friends, In protein lipid simulation , when I do energy minimisation
ster I get an error as " Ek! No confout.gro at all!
Died at inflategro.pl line 104."
What is "confout.gro". If am right it is the output fi
Dear friends, In protein lipid simulation , when I do energy minimisation
ster I get an error as " Ek! No confout.gro at all!
Died at inflategro.pl line 104."
What is "confout.gro". If am right it is the output file that we get from
the minimisation step.
I used the command "
Dear friends, In protein lipid simulation , when I do energy minimisation
ster I get an error as " Ek! No confout.gro at all!
Died at inflategro.pl line 104."
What is "confout.gro". If am right it is the output file that we get from
the minimisation step.
I used the command "
Dear friends, In protein lipid simulation , when I do energy minimisation
ster I get an error as " Ek! No confout.gro at all!
Died at inflategro.pl line 104."
What is "confout.gro". If am right it is the output file that we get from
the minimisation step.
I used the command "
Dear friends, In protein lipid simulation , when I do energy minimisation
ster I get an error as " Ek! No confout.gro at all!
Died at inflategro.pl line 104."
What is "confout.gro". If am right it is the output file that we get from
the minimisation step.
I used the command "
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