I didn't get you. So your problem is solved using trr file or not?
- Message from Lalehan Ozalp -
Date: Tue, 14 Jan 2020 12:53:54 +0300
From: Lalehan Ozalp
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
To: gmx-us
Hii
Have you tried with the .trr file? Try the same procedure with .trr file.
Thanks
- Message from Lalehan Ozalp -
Date: Mon, 13 Jan 2020 13:35:01 +0300
From: Lalehan Ozalp
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
Thank you for your suggestion.
- Message from David van der Spoel -
Date: Thu, 2 Jan 2020 08:28:17 +0100
From: David van der Spoel
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] lifetime of hydrogen bond
To: gmx-us...@gromacs.org
Den 2020-01-02 kl. 07:47, s
Dear all
I want to calculate the hydrogen bond lifetime of a dynamic hydrogen
bond which stays for say 10 ns (as I have saved the trajectory with 10
ps interval). I am trying to calculate the lifetime of this hydrogen
bond by gmx hbond command
gmx hbond -f traj_nopbc.trr -s md.tpr -n index.
Dear all
I have performed a 400 ns mdrun in GROMACS-2016.3. Due to some
problem the job was crushed then I rerun the simulation using
state.cpt file (this happened few more times). The job is finished now
but when I am trying to process the traj.trr file it shows an error
after 20 ns an
Dear all
I have performed a 400 ns mdrun in GROMACS-2016.3. Due to some problem
the job was stopped then I rerun the simulation using state.cpt file
(this happened few more times). The job is finished now but when I am
trying to process the traj.trr file it shows an error after 20 ns and
Hii
I think this is due to the periodic boundary condition. Once you try
to cut the .gro file using -pbc mol by gmx trjconv command. Hope this
will work otherwise it is your system error, you need to modify your
molecule topology file.
- Message from Dhrubajyoti Maji -
Dat
Thank you for your kind reply.
- Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -
Date: Fri, 17 May 2019 13:33:30 +0530
From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water mediated Hbond
To: gmx
Hi
In gmx hbond command there is a flag -ac -contact which gives hbond
autocorrelation function with respect to time. Can I use that to get
idea about lifetime of a Hbond? Because integration of the
autocorrelation function will give the lifetime. Is there anything
wrong?
- Message
Then what is the right way to calculate lifetime of a hydrogen bond?
- Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -
Date: Mon, 13 May 2019 22:24:51 +0530
From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-use
Hi
Then what is the write way to calculate lifetime of a Hbond from gromacs?
- Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -
Date: Mon, 13 May 2019 22:24:51 +0530
From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Reply-To: gmx-us...@gromacs.org
Subject: Re:
Hii
Thank you for your reply. So as u suggest I have to calculate 2 Hbond
separately. But for how long that water mediated Hbond is stable; for
that can I use Hbond number with time? For how many frames both the
bonds appearing together. Is this right? One more thing is that I want
to cal
Dear all
I want to determine the water mediated hydrogen between DNA bases and
small molecule. What extra flag should I use in gmx hbond command? Is
there any other option to capture the water mediated Hbonds? Please
suggest something.
Sunipa Sarkar
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Gromacs Users mailing list
* Please s
Dear all
I want to determine the water mediated hydrogen between DNA bases and
small molecule. What extra flag should I use in gmx hbond command? Is
there any other option to capture the water mediated Hbonds? Please
suggest something.
Sunipa Sarkar
--
Gromacs Users mailing list
* Please s
Hii all
I want to use Amber99 parm bsc1 force field to simulate nucleic acid system
in GROMACS 2016.3. For that I have downloaded amber99bsc1.ff and copy the
folder to gromacs software. Is this right way? Please suggest something. Is
this the right force field for nucleic acids? I am attaching th
- Message from Dr Tushar Ranjan Moharana
-
Date: Thu, 27 Dec 2018 17:01:10 +0530
From: Dr Tushar Ranjan Moharana
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] electrostatic and LJ energy
To: gromacs.org_gmx-users@maillist.sys.kth.se
You can use gmx energy (g_e
- Message from SHAHEE ISLAM -
Date: Thu, 27 Dec 2018 16:52:17 +0530
From: SHAHEE ISLAM
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] how to restart a job in grmacs
To: gmx-us...@gromacs.org
thank you
is the trajectory wil be from 0-15 ns or it will be from
- Message from SHAHEE ISLAM -
Date: Thu, 27 Dec 2018 16:41:21 +0530
From: SHAHEE ISLAM
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] how to restart a job in grmacs
To: gmx-us...@gromacs.org
thank you so much for your reply.
-extend 5000 what does it signif
- Message from SHAHEE ISLAM -
Date: Thu, 27 Dec 2018 16:16:18 +0530
From: SHAHEE ISLAM
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] how to restart a job in grmacs
To: gmx-us...@gromacs.org
hi,
i have run a simulation for 10 ns but after 4 ns due to power off
Hi all
I want to calculate the electrostatic and LJ energy between a part of DNA
and ligand system in GROMACS-2016.3. How to do this? Example: Phosphate -
ligand electrostatic and LJ energy
thanks
Sunipa
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/
Hii all
I want to calculate the binding energy between a biomolecule and ligand. I
have tried installing g_mmpbsa but my gromacs version is 2016.3. Can I
use g_mmpbsa with gromacs-2016.3 or any other way to calculate the binding
energy?
Thanks
Sunipa
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Gromacs Users mailing list
* Please sear
Hii
Thank you for your help. It is working successfully.
Sunipa
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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* For (un)subscribe request
- Message from rajendra kumar -
Date: Mon, 4 Jun 2018 12:23:56 +0200
From: rajendra kumar
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Groove width
To: Discussion list for GROMACS users
I am doing simulation of DNA molecule. I want to calculate groove wi
Hii
I have tried installation of do_x3dna in ubuntu system following the
instructions given in the link. Installation done successfully then I
have written the path of do_x3dna in .bashrc file(export
do_x3dna=/usr/local/do_x3dna/bin/) and source the file source ~/.bashrc.
Then I tried doing do_x3d
Hi all
I want to center my molecule into a rectangular box after final mdrun by
GROMACS. I am using the following command:
gmx trjconv -f traj.trr -s md.tpr -center -pbc mol -b 100 -e 120 -o
test.gro
But output shown is still out of the box. This command works for cubic
box. Is there anything
Hi all
I want to center my molecule into a rectangular box by GROMACS. I am using
the following command:
gmx trjconv -f traj.trr -s md.tpr -center -pbc mol -b 100 -e 120 -o
test.gro
But output shown is still out of the box. This command works for cubic
box. Is there anything different flag fo
Hii David
I want to see if there is any change in the groove width in presence
of different solvents. I thing this can give me some information of DNA
structural change if it is happening in that particular solvent.
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Gromacs Users mailing list
* Please search the archive at
http://www.gro
Thank you for your suggestion. This is a new thing I am learning.
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe req
Hi all
I am doing simulation of DNA molecule. I want to calculate groove width of
DNA in GROMACS. How to do this? Someone please help.
Thanks
Sunipa
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Gromacs Users mailing list
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* Can't
Hii
I want to calculate % of H-bond occupancy between DNA base pair atoms and
Urea molecule in gromacs. Is it possible to do this in gromacs? If not then
what is the way to do that?
Thanks
Sunipa
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http://www.gromacs.org/Support/Mailin
- Message from Peter Stern -
Date: Tue, 24 Apr 2018 07:36:48 +
From: Peter Stern
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] DNA strands are separated
To: "'gmx-us...@gromacs.org'"
Hi,
This is probably just a periodic boundary issue. Use gmx trjco
--- Begin Message ---
Hii all
I am trying to do DNA simulation in water. I have done 200ns mdrun for
that. When I am trying to see the snapshot of different frames in VMD, it
shows that DNA strands are separated and one strand is out of the box. So I
couldn't get the picture of different frames
Hii all
I am trying to do DNA simulation in water. I have done 200ns mdrun for
that. When I am trying to see the snapshot of different frames in VMD, it
shows that DNA strands are separated and one strand is out of the box. So I
couldn't get the picture of different frames with actual solvent
orie
Hii all
I am trying to simulate biomolecule in Guanidinium chloride in
AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking
the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in
energy minimization step but in NVT step files are generated and shows
segmentation
Hii all
I am trying to simulate biomolecule in Guanidinium chloride in
AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking
the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in
energy minimization step but in NVT step files are generated and shows
segmentation
Hii all
I have prepared the topology file for urea molecule in AMBER99sb-ildn force
field taking the parameters from ffbonded.itp and ffnonbonded.itp
available in AMBER folder. After simulation the urea molecule is somewhat
distorted. The N-H bond is tilted. Please suggest me how to solve this
pr
- Message from Mark Abraham -
Date: Fri, 22 Dec 2017 00:42:31 +
From: Mark Abraham
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Hi,
Yes, the parsing of th
- Message from "Jefferies D.F." -
Date: Tue, 19 Dec 2017 20:56:34 +
From: "Jefferies D.F."
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org,
gromacs.org_gmx-users@maillist.sys.kth.se
Out of curiosity, how did yo
- Message from Dhaniram Mahato -
Date: Tue, 19 Dec 2017 21:30:05 +0800
From: Dhaniram Mahato
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org
Hi,
There could be format problem. You can create your own .dat files by
- Message from Dhaniram Mahato -
Date: Tue, 19 Dec 2017 21:30:05 +0800
From: Dhaniram Mahato
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org
Hi,
There could be format problem. You can create your own .dat files by
Hi all
I am doing umbrella sampling taking distance between COM as a reaction
coordinate. when I am trying to calculate PMF using the following command
gmx wham -it tpr-files.dat -if pullf-files.dat -o free.xvg -hist
hist.xvg
I got an error
Program: gmx wham, version 2016.3
Source file:
- Message from João Henriques
-
Date: Sat, 9 Dec 2017 11:29:41 +0100
From: João Henriques
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] DSSP installation
To: gmx-us...@gromacs.org
The output is telling you what is wrong. Gromacs doesn't support version
3.
- Message from João Henriques
-
Date: Sat, 9 Dec 2017 11:29:41 +0100
From: João Henriques
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] DSSP installation
To: gmx-us...@gromacs.org
The output is telling you what is wrong. Gromacs doesn't support version
3.
Hii all
I want to calculate the number of helical contain of protein. For that I
tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
and exported the path to ./bashrc file
export DSSP=/usr/local/bin/ds
Hi all
I want to generate a contact map for all the residues of lysozyme protein.
I am using gmx mdmat to generate this. Can I generate a text file (which
can be open in Grace) except the image files(eg: xpm file)? Please let me
know the particular flag which I can use to get a *.xvg file.
Thanks
- Message from Justin Lemkul -
Date: Fri, 15 Sep 2017 11:12:37 -0400
From: Justin Lemkul
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Binary mixture
To: gmx-us...@gromacs.org
On 9/15/17 10:59 AM, sp...@iacs.res.in wrote:
Hi all
I want to prepare a cubic
Hi all
I want to prepare a cubic box of 6M urea. How many molecules of urea and
how many water molecules should be added to the simulation box? How to
calculate these numbers? Please help me to solve this.
Thanks
Sunipa
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Gromacs Users mailing list
* Please search the archive at
http://www.gr
Hi all
I am trying to do umbrella sampling of protein unfolding with radius of
gyration as reaction coordinate using gromacs-2016.3 patched with
plumed-2.3.2. I want to calculate free energy for the system. I am using
the following command
gmx wham P=1.4 1.5 100 0.001 300 0 metadata.dat free.da
Hi all
I am trying to do umbrella sampling of protein with radius of gyration as
reaction coordinate using gromacs-2016.3 patched with plumed-2.3.2. I have
chosen 13 configurations of protein for sampling. Now I want to analyse the
data. So how to plot histogram and PMF w.r.t radius of gyartion? C
Hii all
I am trying to install plumed-2.3.2 in CRAY system. I am using this
command to configure plumed
./configure --enable-mpi --prefix=/work/plumed-2.2.5/
At the end it shows a warning
configure: WARNING: PLUMED will NOT be compiled using MPI because MPI
have not been found!
configu
I think you can use -cut 0 -rmax 1.5 this will give you the RDF upto 1.5
nm.- Message from "Pandya, Akash" -
Date: Mon, 31 Jul 2017 07:29:19 +
From: "Pandya, Akash"
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] RDF Values
To: gmx-us...@gromacs.org
Hi all,
- Message from Justin Lemkul -
Date: Tue, 25 Apr 2017 10:40:40 -0400
From: Justin Lemkul
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein goes out of the box
To: gmx-us...@gromacs.org
On 4/25/17 10:35 AM, sp...@iacs.res.in wrote:
Hii all,
I have simu
Hii all,
I have simulated protein in 45% ethanol water mixture for 100ns. After
completion of the job I saw that maximum portion of my protein goes out of
the box. Then I have done trjconv -pbc mol to the trajectory file. After
trjconv some portion of the protein is still out of the box. I want to
- Message from Chintan Bhagat -
Date: Wed, 5 Apr 2017 18:42:30 +0530
From: Chintan Bhagat
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] how to know solvent molecule number
To: gromacs.org_gmx-users@maillist.sys.kth.se
Hello,
I want to do stimulation of my pro
- Message from Dilip H N -
Date: Tue, 4 Apr 2017 10:18:23 +0530
From: Dilip H N
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] Regarding getting trajectories in gromacs..
To: gromacs.org_gmx-users@maillist.sys.kth.se
Hello,
I have ran a md simulation for
nsteps
- Message from Mark Abraham -
Date: Tue, 28 Mar 2017 12:04:42 +
From: Mark Abraham
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic
SASA separately in latest version of gromacs?
To: gmx-us...@gromacs.org
H
--- Begin Message ---
Hello,
I am a new user of gromacs. I am trying to calculate SASA for a protein
system. I have used the command
gmx sasa -f traj.trr -s md.tpr -o sasa.xvg -n index.ndx
From this I can only get the total SASA but I want hydrophobic and
hydrophilic SASA separately. I know
- Forwarded message from sp...@iacs.res.in -
Date: Fri, 24 Mar 2017 16:24:21 +0530
From: sp...@iacs.res.in
Subject: How to calculate Hydrophobic and Hydrophilic SASA separately in
latest version of gromacs?
To: gmx-us...@gromacs.org
Hello,
I am a new user of gromacs. I am tryi
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