Hi Mark,
I do not do any equilibration, I only do energy minimization as in the
"GROMACS Tutorial for Solvation Study of Spider Toxin Peptide". Please
let me know if I need to do equilibration and what is the difference
between energy minimization and equilibration as this is not clear to me.
Her
Hi all,
I have a question about how pdb2gmx determines the protonation of the His
residue in default. To best of my knowledge, His usually has its ND1
nitrogen free in un-protonated state, which might equal to the HISB presents
in pdb2gmx. However, when I am treating pdb files by pdb2gmx without
s
>Maximum force = 4.9815813e+24 on atom 169274
You should have a look at that atom, that is a large force.
___
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--- On Thu, 16/7/09, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] Lincs Warning
To: "Discussion list for GROMACS users"
Date: Thursday, 16 July, 2009, 7:30 AM
Samik Bhattacharya wrote:
>
>
> --- On *Wed, 15/7/09, Mark Abraham //* wrote:
>
>
> From: Mark A
Marc Charendoff wrote:
Hello,
I am needing to include a single hydroxide ion in my simulation -
is there a force field available in Gromacs that is already
parameterized, or do I need to create from scratch? With regards to
topology, same question, especially as PRODRG does not do mo
Hello,
I am needing to include a single hydroxide ion in my simulation - is
there a force field available in Gromacs that is already parameterized, or do I
need to create from scratch? With regards to topology, same question,
especially as PRODRG does not do mono or diatomics. Any guidan
Samik Bhattacharya wrote:
--- On *Wed, 15/7/09, Mark Abraham //* wrote:
From: Mark Abraham
Subject: Re: [gmx-users] Lincs Warning
To: "Discussion list for GROMACS users"
Date: Wednesday, 15 July, 2009, 5:23 PM
Samik Bhattacharya wrote:
> Hi all, i ma simulating a
--- On Wed, 15/7/09, Mark Abraham wrote:
From: Mark Abraham
Subject: Re: [gmx-users] Lincs Warning
To: "Discussion list for GROMACS users"
Date: Wednesday, 15 July, 2009, 5:23 PM
Samik Bhattacharya wrote:
> Hi all, i ma simulating a membrane protein, in which i am facing a problem in
> the
Payman Pirzadeh wrote:
Hello,
I have an .pdb file from another simulation. I want to make the appropriate
input files to run a simulations. I have used grompp to produce the .tpr
file, but I get the usual ERROR:
ERROR: The cut-off length is longer than half the shortest box vector or
longer t
I forgot to mention, the dimensions of current simulation box are: 27.154A*
31.354A* 103.386A
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: July 15, 2009 7:24 PM
To: 'Discussion list for GROMACS use
Hello,
I have an .pdb file from another simulation. I want to make the appropriate
input files to run a simulations. I have used grompp to produce the .tpr
file, but I get the usual ERROR:
ERROR: The cut-off length is longer than half the shortest box vector or
longer than the smallest box diagon
darre...@ece.ubc.ca wrote:
Hi Mark,
Yes, I know that the box dimensions are defined in the last line of the
.gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm
in the .gro file.
OK.
I looked through my .gro file to ensure none of the atoms had coordinates
outside the 38x38x
Hi Mark,
Yes, I know that the box dimensions are defined in the last line of the
.gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm
in the .gro file.
I looked through my .gro file to ensure none of the atoms had coordinates
outside the 38x38x38 box. While I was reviewing the f
Thanks a lot That was a big clarification and relief So, my model is
working! Since the RDFs are also correct!
Regards,
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 2:50 P
Payman Pirzadeh wrote:
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 2:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 2:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote:
> -Original Messag
Payman Pirzadeh wrote:
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 2:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote:
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 2:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote:
> Hi,
> I tested TIP4P
Payman Pirzadeh wrote:
Hi,
I tested TIP4P and SPC-E. I used the .gro files in /share/top of the
gromacs. The outputs of energy are:
TIP4P, 1ns npT, T=300K
Energy Average RMSD Fluct. Drift
Tot-Drift
-
Hi,
I tested TIP4P and SPC-E. I used the .gro files in /share/top of the
gromacs. The outputs of energy are:
TIP4P, 1ns npT, T=300K
Energy Average RMSD Fluct. Drift
Tot-Drift
---
Poten
Payman Pirzadeh wrote:
Thanks Justin.
Unfortunately, I realized that after I sent the e-mail. Anyways, I started
running to models: SPCE and TIP4P to check the energies of these systems to
figure out where the problem with my own system (six-site model) could be. I
will keep you posted. But, I h
Thanks Justin.
Unfortunately, I realized that after I sent the e-mail. Anyways, I started
running to models: SPCE and TIP4P to check the energies of these systems to
figure out where the problem with my own system (six-site model) could be. I
will keep you posted. But, I have a question about the
Joseph Johnson wrote:
Is there still a topology and peptide residue on the Gromacs website?
It's mentioned in the documentation but I can't seem to find it.
The user contributions? You can still access all of the old site's content by
appending "old" to the URL (i.e., http://oldwww.groma
quantrum75 wrote:
Dear Gromacs users,
Hi I wanted to ask a begnniner's question regarding protein MD. I have
prior experience with MD simulations through simulating lipid systems.
However I beginning to do some protein MD simulations and wanted the
anyone's advice regarding the forcefields t
Payman Pirzadeh wrote:
Hi again,
I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in
the [atoms ]are specifies as opls_???, doesn't grompp check the database
for the corresponding parameters? Or we should again manually specify the [
atomtypes ] again in either .itp or
Hi again,
I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in
the [atoms ]are specifies as opls_???, doesn't grompp check the database
for the corresponding parameters? Or we should again manually specify the [
atomtypes ] again in either .itp or .top file?
Payman
-O
Is there still a topology and peptide residue on the Gromacs website? It's
mentioned in the documentation but I can't seem to find it.
Thanks :)
_
Hotmail® has ever-growing storage! Don’t worry about storage limits.
http://window
Hi,
Write a (relatively) simple script that reads a pdb file
and prints for each set of three C O O lines two additional O lines: O O C O O.
Gromacs does not care about atom names, and the O positions will be
good enough that the initial constraining in mdrun will correct the mass
positions
to e
OK!
I changed my .top file to
;This is simulation for TIP4P water model
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
; include TIP4P topology
#include "tip4p.itp"
[ system ]
Pure box of water
[ molecul
Hello,
Thanks for the help so far.
I?ve understood the concept of introducing the dummy atoms for linear
molecules with advice and by following an example for acetonitrile
which I found in the user forum (Feb 2003).
I now (hope) that I have an itp file of a have a system of two masses
Dear Gromacs users,
Hi I wanted to ask a begnniner's question regarding protein MD. I have prior
experience with MD simulations through simulating lipid systems. However I
beginning to do some protein MD simulations and wanted the anyone's advice
regarding the forcefields to be used for proteins
jagannath mondal wrote:
Hi,
I was wondering whether one can use a .tpr file made using
gromacs-3.3.1 in gromacs 4.0.5 to restart or exactly continue a
simulation or not.
It should run, but it will not produce a simulation identical with that
produced by 3.3.1. The algorithm is different,
Hi, I was wondering whether one can use a .tpr file made using gromacs-3.3.1
in gromacs 4.0.5 to restart or exactly continue a simulation or
not.ThanksJagannath
Yahoo! recommends that you upgrade to the new and safer Internet Explorer
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Dear gmx users
When simulating the process of surfactant self-assembly, is there any
specific consideration in converting the trajectory to a continuous form? I
read in the mailing list that in the simulation of clusters (such as
micelles) the molecules must be whole in the reference structure (tp
Try using trjconv. Look at the -pbc options and also maybe -center options.
--Omer.
Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Wed, Jul 15, 2009 at 10:09, nikhil damle wrote:
> but peptide remains inside the
Samik Bhattacharya wrote:
Hi all, i ma simulating a membrane protein, in which i am facing a
problem in the equilibration step. in the NVT equilibration when i am
running the mdrun command i am getting a msg like
Program mdrun, VERSION 4.0.5
Source code file: constr.c, line: 136
Fatal error:
Hi all, i ma simulating a membrane protein, in which i am facing a problem in
the equilibration step. in the NVT equilibration when i am running the mdrun
command i am getting a msg like
Program mdrun, VERSION 4.0.5
Source code file: constr.c, line: 136
Fatal error:
Too many LINCS warnings (19
Think outside of the box when using Periodic Boundary Conditions. :p
Tsjerk
On Wed, Jul 15, 2009 at 9:14 AM, Mark Abraham wrote:
> nikhil damle wrote:
>>
>> Hello,
>>
>> When I am running energy minimisation of protein-peptide complex,
>> minimised structure shows a space for the protein in wate
nikhil damle wrote:
Hello,
When I am running energy minimisation of protein-peptide complex,
minimised structure shows a space for the protein in water box; but
peptide remains inside the box while protein is seen outside.
Same occurs when I keep pbc = xyz and/or nstcomm = 1
in ..top file,
Hello,
When I am running energy minimisation of protein-peptide complex, minimised
structure shows a space for the protein in water box; but peptide remains
inside the box while protein is seen outside.
Same occurs when I keep pbc = xyz and/or nstcomm = 1
in .top file, I am including individua
darre...@ece.ubc.ca wrote:
Hi Justin,
I was experiencing the problem before someone suggested using editconf so
I do not think the problem is being caused by editconf. But anyway here
is my editconf command. Let me know if you a source of error in this
command line.
editconf -f graphene.gro -n i
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