Hi all,
I have something here which I am would like to pick your brains. Thank
you in advance. In my trial-and-error attempt to equilibrate my membrane
protein system, I encountered this problem.
I was playing with 2 different mdp files (in succession), first by using
the Nose Hoover then v
Dear gmxusers,
I have some questions about distance restraints that I hope you would be able
to shed some light on. Thanks in advance.
I am trying to apply distance restraints to my protein. Below was what I did:
-use genrestr to create my ca_disre.itp
genrestr -f membedded_em.gro -o ca_disre.
through the information in the .tpr file given by
gmxdump to see if they are indeed properly defined.
Cheers,
Tsjerk
On Jan 18, 2012 1:46 AM, "NG HUI WEN"
mailto:huiwen...@nottingham.edu.my>> wrote:
Dear gmxusers,
I have some questions about distance restraints that I hope y
users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of NG HUI WEN [huiwen...@nottingham.edu.my]
Sent: 18 January 2012 16:40
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] questions on distance restraints
Dear Tsjerk,
Thanks very much indeed for confirming this, rea
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] questions on distance restraints
NG HUI WEN wrote:
> Dear all,
>
>
>
> Apologies for getting back to this topic again - am still having trouble
> trying to get distance restraints to work on my protein.
>
>
>
From: NG HUI WEN
Sent: Sunday, February 19, 2012 1:19 PM
To: gmx-users@gromacs.org
Subject: Distance Restraints on Protein - possible at all?
Dear gmxusers,
I have been trying to apply distance restraints on my protein but have been
unsuccessful thus far.
I have consulted the user forum
AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Distance Restraints on Protein - possible at all?
On 22/02/2012 11:17 AM, NG HUI WEN wrote:
From: NG HUI WEN
Sent: Sunday, February 19, 2012 1:19 PM
To: gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>
Subject: Distance Restraints
Hi all,
I have a seemingly simple task that turned quite tricky here.
I am trying to perform energy minimization on a crystal structure after adding
hydrogen to the protein using pdb2gmx (OPLS).
The problem I am facing now is that after energy minimization, the protein and
water (origina
crystal structure with water
On 18/03/2012 1:01 PM, NG HUI WEN wrote:
Hi all,
I have a seemingly simple task that turned quite tricky here.
I am trying to perform energy minimization on a crystal structure after adding
hydrogen to the protein using pdb2gmx (OPLS).
The problem I am facing now
Hi gmxusers,
Hope you are well. I am trying to apply position restraints to my crystal
waters (just briefly, 1-2ns) but have been unsuccessful.
Taking into account the advice from this thread
http://lists.gromacs.org/pipermail/gmx-users/2012-February/068780.html, this
was what I had done:
sys
Dear all,
I have a follow up question from this recent post
http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html regarding the
visualization of g_helixorient output.
According to the post, one needs to use xmgrace with -nxy to view the data
properly. I have not got the xmgrace progr
gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Mark Abraham
Sent: Thursday, November 24, 2011 10:39 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Visualizing g_helixorient output
On 23/11/2011 8:59 PM, NG HUI WEN wrote:
Dear all,
I have a follow u
Dear Gmxusers,
I have noticed that energy minimization with gromacs (gromos G53a6
forcefield) had led to the distortion of sidechain planarity in my
protein model. Comparison of PROCEHCK results between the pre- and post
energy minimized structures have shown an increase in the number of
distor
sers-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of NG HUI WEN
> Sent: 20 September 2010 04:21
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Energy Minimzation with Gromacs leads to
distortion of planar groups
>
> Dear Gmxusers,
>
> I have noticed
omacs leads to
distortionofplanar groups
NG HUI WEN wrote:
> Hi
>
> Thanks a lot for the suggestions.
>
> I removed -DFLEXIBLE this time but it still didn't work unfortunately.
I
> started off with 0 distorted planar group and ended up with 38 after
> minimization (sa
Dear gmxusers,
I am trying to make a lipid bilayer with specific dimensions using
gromacs. So far, I have got up to:
1) Download a lipid POPC128a.pdb from Peter Tieleman's website
2) Use genconf -f popc128a.pdb -o popcx2.pdb -nbox 2 2 1 to
multiply the lipid in the x and y ax
00:32 CEST 2010
* Previous message: [gmx-users] How to make a lipid bilayer with
specific dimensions?
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deprotonation of some residues
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NG HUI WEN wrote:
> Dea
with specific
dimensions?
NG HUI WEN wrote:
> Thanks for that guys! I will try them out.
>
> Just a quick question here with regards to my lipids being possibly
too
> small, does it have something to do with the minimum image criterion
> for PBC? I have ensured that the distance
Dear gmxusers,
I have obtained a box of POPC with a starting dimension of 12.48, 12.36, and
6.92 (nm) using genconf -nbox 2 2 1. The original lipid was downloaded from
Prof. Tieleman's site (popc128a.pdb).
My intention is to equilibrate the new bilayer such that the lipids,
particularl
molecules jump
outof box
NG HUI WEN wrote:
> Dear gmxusers,
>
>
>
> I have obtained a box of POPC with a starting dimension of 12.48,
12.36,
> and 6.92 (nm) using genconf -nbox 2 2 1. The original lipid was
> downloaded from Prof. Tieleman's site (popc128a.pdb)
Dear GMXusers,
I am trying to perform NVT on my solvated protein-lipid system. After
inserting the protein into the lipid using inflategro and a round of
energy minimization, I performed a 100ps NVT with position restraint
only on the protein molecule using (posre.itp).
After 100ps of NVT,
Hi Gmxusers,
I have been trying to run mdrun -rerun to get the energy of the protein
in my protein-lipid system. I know similar questions have been raised on
this topic before, I have tried to glean useful information from them to
solve my problem but unfortunately to no avail. Thanks for your
run -rerun: bonded interactions of protein
On 10/11/2010 11:29 PM, NG HUI WEN wrote:
Hi Gmxusers,
I have been trying to run mdrun -rerun to get the energy of the protein
in my protein-lipid system. I know similar questions have been raised on
this topic before, I have tried to glean useful i
Dear gromacs users,
I have a protein embedded in a lipid bilayer. After sufficient
equilibration of the system ( i.e. size of box X and Box Y became quite
constant), I would now like to assess the area per lipid of my system.
However, (I think) I could not simply do this ( average size o
n list for GROMACS users
Subject: Re: [gmx-users] mdrun -rerun: bonded interactions of protein
On 11/11/2010 7:46 PM, NG HUI WEN wrote:
Thanks a lot Justin and Mark for your useful input.
Indeed Justin was right, the quest to dissect the total energy of the
system to get that contribu
: RE: [gmx-users] mdrun -rerun: bonded interactions of protein
Quoting NG HUI WEN :
> Dear Mark and Justin,
>
>
>
> I have a potentially silly question here. I have been trying to work
out
> the figures from the various options of g_energy. You mentioned before
> that the
Try POP instead of POPE :)
From: gmx-users-boun...@gromacs.org on behalf of shikha agarwal
Sent: Thu 12/23/2010 4:21 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Illegal division by zero at inflategro
Hi
I am having a trouble during inflategro sc
Dear all,
Merry Xmas! I have a very quick question here which i'd like to pick your brain
on, would really appreciate a reply.
I am planning to replicate an experiment that I have carried out. Just
wondering what is the best way to do it? I am thinking of changing the starting
velocity of
David van der Spoel
Sent: Sat 12/25/2010 10:28 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Replicating an experiment
On 2010-12-25 15.05, NG HUI WEN wrote:
> Dear all,
> Merry Xmas! I have a very quick question here which i'd like to pick
> your brain on,
Got it, thanks very much David!
:)
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel
Sent: Sun 12/26/2010 5:55 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Replicating an experiment
On 12/25/10 6:37 PM, NG HUI WEN wrote
/2010 4:37 AM, NG HUI WEN wrote:
> Thank you David for your prompt and useful reply :) I am in fact
simulating a membrane protein.
>
> It's good to know I can use the "generate-new-starting-velocity"
method. But, do you mind to elaborate a bit more what you mean by &quo
Dear all,
This must be a pretty simple problem but I am stuck nonetheless. I have been
using the lipids from Prof Tieleman's website without any problem on gromacs
4.0.7.
Now that I've got 4.5.3 installed, I want to try the g_membed tool but have
encountered these problems.
Following Just
Oops sorry!
I found the mistake...
the topology file should read
"gromos53a6_lipid.ff/forcefield.itp" instead of "gromos53a6.ff/forcefield.itp"
silly me
From: gmx-users-boun...@gromacs.org on behalf of NG HUI WEN
Sent: Sun 1/23/2011 1
would have gotten this if you had chosen the proper force field with
pdb2gmx. Option 1 (which includes the Berger lipids) is the correct one.
Option 14 is the vanilla Gromos96 53a6 force field, which is not what you want.
-Justin
> silly me
>
> -------------
ailto:gmx-users-boun...@gromacs.org] On
Behalf Of Justin A. Lemkul
Sent: Monday, January 24, 2011 10:14 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3
NG HUI WEN wrote:
> Dear Justin,
>
> Thanks for pointing out :) much appreciated.
>
It worked! Thanks very much again for your time and help.
Cheers,
huiwen
-Original Message-
From: Justin A. Lemkul [mailto:jalem...@vt.edu]
Sent: Tuesday, January 25, 2011 8:49 AM
To: NG HUI WEN; Gromacs Users' List
Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3
Dear gmxusers,
I have a question here concerning nstcomm.
I got the note below after doing grompp, I'd like to do something about
it.
NOTE 1 [file HW_NPT.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Currently, my nstcomm is
Hi,
I'm a new gromacs user. I have encountered a problem with pdb2gmx where
it automatically renumbers the residues in my pdb file.
For instance, the first residue in my protein F8 has become F1 - this
affects all the residues in the protein, something I find rather
inconvenient.
I've
y pdb file
- Original Message -
From: NG HUI WEN
Date: Thursday, June 3, 2010 18:08
Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file
To: gmx-users@gromacs.org
> Hi,
>
> I'm a new gromacs user. I have encountered a problem with pdb2gmx
where it auto
Dear gmxusers,
I have a very basic question here which I hope someone could help me with. I
was running a couple of simulations over the weekend on a shared cluster and
both came to a stop for the same reasons:
Program mdrun_mpi, VERSION 4.0.7
Source code file: trnio.c, line: 252
File input/o
Hi guys
Thanks for your help! I will consider your suggestions.
Huiwen
From: NG HUI WEN
Sent: Monday, August 09, 2010 11:05 AM
To: gmx-users@gromacs.org
Subject: Large output files and limited disk space. How do I handle
them?
Dear gmxusers,
I have a very basic question here
Hi,
I have been playing with the "mdrun_mpi" command in gromacs 4.0.7 to try out
parallel processing. Unfortunately, the results I got did not show any
significant improvement in simulation time.
Below is the command I issued:
mpirun -np x mdrun_mpi -deffnm
where x is the number of proc
ficult to scale.
You might want to try the 4.5beta version because we have improved the
scaling with it. Also there is a tool g_tune_pme which might help you.
Roland
________
From: NG HUI WEN
Sent: Mon 8/23/2010 11:15 PM
To: gmx-users@gromacs.org
Subject: Attempting t
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