Dear Gromacs Users,
I want to know that if there is a easy way of using GLYCAM force field in
Gromacs. Thanks in advance!
Best regards
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On 5/22/17 4:59 PM, Pandya, Akash wrote:
Sorry I meant 20 A. But I'll look into expanding the box size and see if it
works. Thanks for your help.
Making the box larger is unlikely to be useful. You should simplify the system
by simulating individual components as the link I provided befor
One quick question what would you suggest a suitable box size is?
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: 22 May 2017 21:52
To: gmx-us...@gromacs.org
Subject: R
Sorry I meant 20 A. But I'll look into expanding the box size and see if it
works. Thanks for your help.
Akash
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: 22 May 2
On 5/22/17 4:42 PM, Pandya, Akash wrote:
Is there a chance that as my simulation box is quite small 2 angstroms and
citrate is a charged anion, this could be a cause of my system blowing up?
I don't see how any sensible system can be that small. Are you sure it's 2 A
and not 2 nm? Even 2
Is there a chance that as my simulation box is quite small 2 angstroms and
citrate is a charged anion, this could be a cause of my system blowing up?
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] O
On 5/22/17 10:00 AM, Sailesh Bataju wrote:
Hi Sir,
Right, CHARMM force field is what I'm looking for. Thank you very much
sir for your advice. I've made parameter file of isobutane using
CHARMM36 force field files shown below so I've a few questions
regarding it.
[ defaults ]
; nbfunc
Hi Dallas,
Thanks for your reply.
I did try -pbc cluster for waters. It could fix it somehow but not
completely.
After that, I had to use -pbc center to fix it. Still, I do not get what I
want.
Unfortunately, some waters and lipids are appearing from the other side of
the box.
Cheers,
Mohsen
On
Hi Sir,
Right, CHARMM force field is what I'm looking for. Thank you very much
sir for your advice. I've made parameter file of isobutane using
CHARMM36 force field files shown below so I've a few questions
regarding it.
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
On 5/22/17 7:25 AM, Pandya, Akash wrote:
What could be wrong with the topology could you please elaborate? I added
glycine and citrate molecules to the simulation box randomly. Could it be the
fact I added topology for glycine and citrate in the wrong way?
This is how my topol.top file look
What could be wrong with the topology could you please elaborate? I added
glycine and citrate molecules to the simulation box randomly. Could it be the
fact I added topology for glycine and citrate in the wrong way?
This is how my topol.top file looks:
; Include Citrate Topology
#include "Citr
On 5/22/17 6:55 AM, Jai Krishna wrote:
Dear Sir/Ma'am,
I am trying to generate topology file for my metalloprotein that has FeS
cluster and Fe2+ atoms in it. When I run the pdb2gmx command, it fails to
generate the topology file. The error says - Residue 'FE2' not found in
residue topology d
On 5/22/17 6:47 AM, Pandya, Akash wrote:
Hi all,
During Minimisation I get the following output that the simulation ended
prematurely.
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps= 50
Step=0, Dmax= 1.0e-02 nm, Epot= 7.39413e+26 Fmax=
On 5/22/17 6:47 AM, ZHANG Cheng wrote:
Dear Joao,
Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that
true that NVT needs to change two lines, while NPT and production run only need
to change one line?
Yes.
-Justin
Yours sincerely
Cheng
1) In the NVT:
ref_t =
Okay,
Thank You
*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
On Mon, May 22, 2017 at 5:17 PM, Peter Kroon wrote:
> Hi,
>
>
> we are aware of it and will probably fix it later today. It's an update
> gone wrong.
>
>
> Peter
>
>
> On
Dear Sir/Ma'am,
I am trying to generate topology file for my metalloprotein that has FeS
cluster and Fe2+ atoms in it. When I run the pdb2gmx command, it fails to
generate the topology file. The error says - Residue 'FE2' not found in
residue topology database.
Could you please help me with thi
Hi,
we are aware of it and will probably fix it later today. It's an update
gone wrong.
Peter
On 22-05-17 11:44, Anurag Dobhal wrote:
> Hello Gromacs users,
>
> This query is not related to typical gromacs error. I am unable to access
> the Martini Forcefield website (http://cgmartini.nl/) fr
Dear Joao,
Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that
true that NVT needs to change two lines, while NPT and production run only need
to change one line?
Yours sincerely
Cheng
1) In the NVT:
ref_t = 370 370 ; reference temperature, one for each grou
Hi all,
During Minimisation I get the following output that the simulation ended
prematurely.
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps= 50
Step=0, Dmax= 1.0e-02 nm, Epot= 7.39413e+26 Fmax= inf, atom= 6640
Step= 14, Dmax= 1.2e-06 n
On 5/22/17 1:09 AM, Mohammad Hassan Khatami wrote:
Hi Justin,
I am asked to focus on learning how to change and update the CHARMM36
parameters, so I could implement the future changes and patches easier. (Thus,
I am not focused in the Glycan Reader, at the moment.)
Thank you! I think I now h
On 5/22/17 4:04 AM, abhisek Mondal wrote:
I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) a
You haven't adjusted the temperature on the production mdp file, it's still
300 K.
J
On Mon, May 22, 2017 at 12:37 PM, ZHANG Cheng <272699...@qq.com> wrote:
> Dear Gromacs,
> I am performing 370 K MD based on Justin's tutorial.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tu
Dear Gromacs,
I am performing 370 K MD based on Justin's tutorial.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
After "Step Five: Energy Minimization", I need to do NVT, NPT and a production
run.
I think I need to change 300 K to 370 K in three md
Hello Gromacs users,
This query is not related to typical gromacs error. I am unable to access
the Martini Forcefield website (http://cgmartini.nl/) from the past few
days. I just wanted to know if any of the gromacs users are aware of this
issue ? am I opening the right website ?
Thank you
*A
Dear All,
I am trying to calculate the tetrahedral orientational order parameter
using command g_hydorder. I get two output with option -or option which is
of the type -
0 0 2.92500
0 1 2.92500
0 2 2.92500
0 3 2.92500
0 4 2.92500
0 5 2.92500
0 6 2.92500
0 7 2.92500
0 8 2
I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) and applied as pull-coord1-vec.
However, I hate
Hi dear gmx-users
Iwant to simulate gold surface - protein interaction by GOLP-CHARMM
forcefield.In md step, after 7 ps , without any reason mdrun failed. md.mdp
contains:
title = gold
cpp =cpp
include =
;RUN CONTROL PARAMETERS
integr
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