ubject: Re: [gmx-users] pull code
Poojari, Chetan wrote:
> Hi,
>
> I am using umbrella sampling to pull my peptide (peptide starting from above
> the lipid bilayer) into the hydrophobic core of the lipid bilayer.
>
> Following are my inputs i have used:
>
> title
mkul [jalem...@vt.edu]
Sent: 10 February 2011 12:33
To: Gromacs Users' List
Subject: Re: [gmx-users] pull code
Poojari, Chetan wrote:
> Hi Justin,
>
> Thank you very much for your suggestions. I will use constraint force to
> force a peptide into a membrane with pulling for longer
Hi,
I am doing Dihedral PCA and followed the steps as mentioned in the Gromacs
documentation http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
Below are the commands i used:
1) I generated index file for chosen dihedral angles.
2) g_angle -f 100ns_noPBC.xtc -n dangle.ndx -or dangle.tr
Hi,
I am using Gromacs 4.5.3 and want to extend my umbrella sampling runs.
But i get an errror while running the "mdrun" step of extension command, saying
"Start of file magic number mismatch, checkpoint file has 1993, should be
171817. The checkpoint file is corrupted or not a checkpoint file"
Hello Chris,
Thank you very much for your reply. I have done following test as you suggested
to check whether the checkpoint file are corrupted.
1) Yes, I have used same version of gromacs for mdrun and to produce .cpt file.
2) when i do gmxcheck -f 0.cpt # i get the same error.
Hello Chris,
I followed the steps as mentioned in the umbrella sampling tutorial in gromacs.
After NPT equilibration step, i did the umbrella simulation runs. Below are the
commands which i used:
grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o
umbrella0.tpr
mdr
September 2011 14:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] check point file corrupted - umbrella sampling
Justin A. Lemkul wrote:
>
>
> Poojari, Chetan wrote:
>> Hello Chris,
>>
>> I followed the steps as mentioned in the umbrella sampling tutorial in
...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 20 September 2011 15:05
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] check point file corrupted - umbrella sampling
Poojari, Chetan wrote:
> Hello Justin,
>
> Thank you very much for your reply.
>
> I mus
Hi,
I want to calculate order parameter for POPC lipid.
After reading the comments made by Justin and Chris about g_order, i would like
to compare my results from both g_order and vmd tcl script which will compute
order parameters from real hydrogen atoms.
Below is the link I found for vmd tc
Hi,
I have protein completely inserted into lipid membrane and would like to study
order parameter around the protein as well as away from the protein.
For this I would like to slice my membrane into parts.
I tried the following command:
g_order -s *.tpr -f *.xtc -n sn1.ndx -d z -od deuter_sn1
good luck,
> igor
>
>
> Igor Marques
>
>
> On Tue, Oct 11, 2011 at 6:20 PM, Poojari, Chetan
> mailto:c.pooj...@fz-juelich.de>> wrote:
>
> Hi,
>
> I have protein completely inserted into lipid membrane and would
> like to study order
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 14 October 2011 12:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] lipid membrane slicing
Poojari, Chetan wrote:
> Thank you Justin, Igor for y
ds,
chetan.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 17 October 2011 20:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] lipid membrane slicing
Pooja
Hi,
I want to extend the umbrella sampling runs and have used the below commands:
1) grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx
-o umbrella0.tpr
2) mdrun -s umbrella0.tpr -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo
0.cpt -c 0.gro -x 0.xtc -g 0.log -
Hi,
I want to extend the umbrella sampling runs and have used the below commands:
1) grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx
-o umbrella0.tpr
2) mdrun -s umbrella0.tpr -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo
0.cpt -c 0.gro -x 0.xtc -g 0.log
Hi,
I have a peptide inserted in membrane would like to analyze the peptide tilt.
The command i have used to do this is :
g_helixorient -s .tpr -f .xtc -n .ndx -otilt
Index file contains all carbon alpha atoms of the helix.
When i plot the tilt.xvg in xmgrace, i simply cannot obtain anyth
Dear All,
I want to calculate interaction energy per residue.
Below is the command i used:
g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm
my groups.dat file contains these lines:
3
strand1_SER_34
strand1_THR_36
strand1_TYR_37
When i execute the above g_enemat command i get
Hello Justin,
I wanted to find the probability of hydrogen bond formed between my peptide and
water molecules over time. So I used your plot_hbmap.pl script.
As mentioned in the script file, my index file contained atom numbers only from
the [hbonds...] section, rest were deleted.
Heres my sh
...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
> Hello Justin,
>
> I wanted to find the probability of hydrogen bo
Kind regards,
chetan.
___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:06
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
> Hello
lf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:54
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
> Hello Justin,
>
> I commented out the lines from 151-161
>
> # unless ($resn =~ /SOL/) {
...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 22:48
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
> Hello Justin,
>
> I commented out line 151 and braces enclosing it.
>
&g
Hi,
I am following the umbrella sampling tutorial written by Justin Lemkul.
I was successfully able to run the umbrella sampling simulations, but for each
configuration it outputted a single xvg file.
For the data analysis i should have pullf.xvg / pullx.xvg filesbut these
files are not ou
Hi,
Following were the commands which i used in the umbrella sampling simulations:
grompp -f md_umbrella.mdp -c conf500.gro -p topol.top -n index.ndx -o
umbrella500.tpr
mdrun -v -deffnm umbrella500
Output:umbrella500.xvg, umbrella500.xtc, umbrella500.trr, umbrella500.log,
umbrella500.gro
Dec 16, 2010, at 2:23 PM, Poojari, Chetan wrote:
> Hi,
>
> Following were the commands which i used in the umbrella sampling simulations:
>
> grompp -f md_umbrella.mdp -c conf500.gro -p topol.top -n index.ndx -o
> umbrella500.tpr
>
> mdrun -v -deffnm umbrella500
>
>
Hi,
I am doing data analysis of umbrella sampling tutorial. I have created 2 files :
a) tpr-files.dat (under this folder i got )
144.tpr
169.tpr
300.tpr
400.tpr
500.tpr
b) pullf-files.dat
pullf144.xvg
pullf169.xvg
pullf300.xvg
pullf400.xvg
pullf500.xvg
When i run this command:
g_wham -it t
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 16 December 2010 20:49
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] tpr-files.dat and pullf-files.dat
Poojari, Chetan wrote:
> Hi,
>
> I am doing data analysi
Hi,
I am following umbrella sampling tutorial for my membrane protein system.
While running continuous pulling simulation (mdrun). under step five:
Generating Configurations of the tutorial. I get the below error.
The system ran initially but corrupted very soon with warning " The X-size of
Hi,
To my earlier post on number of DD cells.i included -dds 0.6 and everything
seems to run fine.
Is this the possible solution to the error or is there other way to handle this
warning ?
Kind regards,
chetan.
---
Hi,
I am working on membrane protein.
In umbrella sampling tutorial...we saw the pulling of the peptide A away
from peptide B.
I want to pull the peptide deep into the hydrophobic core of the bilayer from
outside (solvent environment).
Please can someone suggest me how to go about this.
-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: 27 December 2010 00:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] number of DD cells
On 27/12/2010 7:51 AM, Poojari, Chetan wrote:
> Hi,
>
> I am
Hi,
I am using umbrella sampling to pull my peptide (peptide starting from above
the lipid bilayer) into the hydrophobic core of the lipid bilayer.
Following are my inputs i have used:
title = Umbrella pulling simulation
define = -DPOSRES_LIPID
; Run parameters
integrator
Hi,
I have done MD simulations of membrane-protein. I want to calculate interaction
energies between protein and headgroup, protein and hydrophobic core (in the
bilayer).
Please can anyone suggest me the method that should be followed to carry out
these analysis.
kind regards and best wishes,
Hi,
I have completed membrane protein simulations. I want to do some free energy
calculations but haven't included energygrps in the mdp file.
Please can someone suggest me if theres a way to generate separate energygrps
for my protein and lipid now as I carried out simulations without having
Hi,
I am doing rerun to calculate LJ-SR & coul-SR interactions and other energy
terms for energygrps defined in mdp file.
I have constrained all bonds with lincs algorithm in mdp file.
While running rerun i get following warnings
WARNING: Some frames do not contain velocities.
...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: 16 September 2010 12:12
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] rerun warning
- Original Message -
From: "Poojari, Chetan"
Date: Thursday, September 16, 2010 20:
. Lemkul [jalem...@vt.edu]
Sent: 16 September 2010 12:35
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] rerun warning
Poojari, Chetan wrote:
> Hello Mark,
>
> Thank you very much for quick reply.
>
> I am looking for LJ and coul interactions, please can i know what ca
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