Hello Justin Lemkul,
Thank you for the suggestions. I understood and already tried using
transforms with trjconv. The picture got better.
--
Message: 4
Date: Thu, 7 May 2020 08:17:06 -0400
From: Justin Lemkul
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users]
Hello Debashish,
Thank you for the suggestions.
Could you tell us in more detail how (in which file) postion restraints
on them in x, y, z should be written by putting force constant of [1000
1000 1000
Could you please advise the links where I can read about it?
Message: 3
Date: Thu, 7 May
Hi Nikhil,
Lazaro Andres Monteserin Castanedo (lamonteserincastan...@gmail.com) invited
you to view the file " gibbs-1_2.xpm " on Dropbox.
View file[1]
Enjoy!
The Dropbox team
[1]: https://www.dropbox.com/l/scl/AADRnq_Zod0PzsbuSrY9eQBYX4o2QtoeR9U
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* Please
Hello gmx users!
As announced in my previous message at the beginning of the week, we
will be activating the new discussion forum today.
At the same time, the mailing list will move to read-only mode, so
please don't be surprised when it is no longer possible to submit new
messages to it.
Dear Gromacs users,
I am trying to run a simulation annealing using Gromacs of a small
molecule. Does anybody knows if there is a protocol to set up the annealing
parameters for Gromacs; initial temperature, final temperature,
annealing-npoints, annealing-ntimes and the annealing-temp? My total
Cs
:
:
:
:
:
/ **:***/
Dear all,
In a PMF simulation using WHAM, the windows are somehow that the reaction
coordinate (RC = COM_group1 COM_group2) should have both positive and
negative parts along Z direction, e.g COM_group1 locates in the middle of
the reaction coordinate more or less. However, what the WHAM
Hello gmx users,
I am stuck at a very basic command line and need your expertise in dealing
through it.
Basically, I have a clay sheet containing 192 surface oxygen. Since I am
doing umbrella sampling for PMF calculations, I want to get the progression
of COM distances of my fixed Cs atom from
Hello gmx users,
I am stuck at a very basic command line and need your expertise in dealing
through it.
Basically, I have a clay sheet containing 192 surface oxygen. Since I am
doing umbrella sampling for PMF calculations, I want to get the progression
of COM distances of my fixed Cs atom from
On 5/7/20 10:57 AM, Devargya Chakraborty wrote:
I think I couldn't frame the question correctly. Let's say I have a silica
surface and I have water droplet on it and after a proper nvt simulation I
want to calculate the interaction energy of the water droplet with the
surface then how can I
I think I couldn't frame the question correctly. Let's say I have a silica
surface and I have water droplet on it and after a proper nvt simulation I
want to calculate the interaction energy of the water droplet with the
surface then how can I use the energy grps option for analysis.
Thanks
On 5/7/20 10:49 AM, Devargya Chakraborty wrote:
Suppose my system contains an anion a cation and water and I have done an
nvt simulation.after the completion I want to see the energy profile of the
individual groups like the cation or the anion etc. Can anybody guide me
how to use the energy
Suppose my system contains an anion a cation and water and I have done an
nvt simulation.after the completion I want to see the energy profile of the
individual groups like the cation or the anion etc. Can anybody guide me
how to use the energy grps option in analysing that.
Thanks
Devargya
Thanks Justin. I will then add manually the constraints on the topology
file.
Paolo
Il giorno gio 7 mag 2020 alle ore 14:56 Justin Lemkul ha
scritto:
>
>
> On 5/7/20 8:53 AM, Paolo Costa wrote:
> > Dear Justin
> >
> > that means when I generate the topology file by pdb2gmx I will add
>
Dear Justin
that means when I generate the topology file by pdb2gmx I will add manually
the section [constraints] on it?
Thanks.
Paolo
Il giorno gio 7 mag 2020 alle ore 14:50 Justin Lemkul ha
scritto:
>
>
> On 5/7/20 8:47 AM, Paolo Costa wrote:
> > Dear Justin,
> >
> > I thought too.
> > In
On 5/7/20 8:53 AM, Paolo Costa wrote:
Dear Justin
that means when I generate the topology file by pdb2gmx I will add manually
the section [constraints] on it?
I suggest you look into the manual to understand different ways of
applying constraints. You can either convert bonds into
On 5/7/20 8:47 AM, Paolo Costa wrote:
Dear Justin,
I thought too.
In case, could you please indicate me how I can constrain the interatomic
distance of a desired molecule, in such case the POM molecule?
Define [constraints] in the topology for all relevant interatomic distances.
-Justin
Dear Justin,
I thought too.
In case, could you please indicate me how I can constrain the interatomic
distance of a desired molecule, in such case the POM molecule?
Thanks a lot.
Paolo
Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul ha
scritto:
>
>
> On 5/7/20 8:41 AM, Paolo Costa
On 5/7/20 8:41 AM, Paolo Costa wrote:
Dear Justin,
thanks a lot for your valuable information.
The system (Keggin anion, POM) I am trying to simulate is almost identical
to the one already studied in literature (doi: 10.1021/jp077098p).
In the SI of this work, the authors stated "*Keggin
Dear Justin,
thanks a lot for your valuable information.
The system (Keggin anion, POM) I am trying to simulate is almost identical
to the one already studied in literature (doi: 10.1021/jp077098p).
In the SI of this work, the authors stated "*Keggin anions are treated as
rigid particles thus
Hello Justin, so I believe it's just pbc visualization stuff going on
then.. okay.. yes you can do it then from trjconv .
Regards,
Debashish
On Thu, 7 May 2020, 14:14 Debashish Banerjee,
wrote:
> Hello Ekatherina, I did not reach a point in my simulations where I have
> used freeze command,
On 5/6/20 11:35 AM, Paolo Costa wrote:
Dear Gromacs users,
I am interested on studying the interaction between large metal cluster
anions (polyoxometallates, POM) with different organic cations (e.g
perylenes, etc..) in water.
I have already the non bonded parameters of POMs from literature,
On 5/6/20 6:31 PM, Lei Qian wrote:
Dear users,
I know interaction energy calculation is carried out via energygrps setting
in mdp file.
Because free energy-related settings do not include this energygrps
setting, so I think this energygrps setting may NOT be related to free
energy settings.
On 5/7/20 4:24 AM, Ekatherina O wrote:
Hello Dr. Dallas Warren,
Thank you for the suggestions.
But this does not solve the problem of the movement of atoms of quartz
layers (upper and lower) located at the borders of the box. I would
like the quartz layers to remain intact during the
Hello Ekatherina, I did not reach a point in my simulations where I have
used freeze command, but I think for your case, can't you put a position
constraint on your quartz layer. In that case, you just have to create an
index file having quartz in the group and then you can put postion
restraints
Many thanks Alex for your reply :)
You have pressure scaling and LINCS convergence issues, suggesting that
> the starting configuration is far from equilibrium, as well as
> potentially other issues.
>
> How to check if my starting configuration is far from equilibrium ? I
checked the Temperature
Many thanks david for the explanation.
In did NVT then NPT equilibiration and then the production run, in the
production run .mdp file I have the same parameters as in NVT and NPT.mdp
files. Does this mean that my simulation is a NVT simulation or NPT ?
Is it possible to do only one of them (NVT
Hello Dr. Dallas Warren,
Thank you for the suggestions.
But this does not solve the problem of the movement of atoms of quartz
layers (upper and lower) located at the borders of the box. I would like
the quartz layers to remain intact during the modeling process, i.e.
atoms did not move and
Dear users,
I know interaction energy calculation is carried out via energygrps setting
in mdp file.
Because free energy-related settings do not include this energygrps
setting, so I think this energygrps setting may NOT be related to free
energy settings.
Could I ask whether my idea is correct
Dear Gromacs users,
I am interested on studying the interaction between large metal cluster
anions (polyoxometallates, POM) with different organic cations (e.g
perylenes, etc..) in water.
I have already the non bonded parameters of POMs from literature, while the
bonded parameters I calculated
Den 2020-05-06 kl. 10:21, skrev Mohamed Abdelaal:
Yes I measured both, the density and the free volume using gromacs.
Since the free volume changes with respect to time, shouldn’t the density
also change with time ?
What do you mean with "changes"? If the density is constant (with
I started with NVT then NPT then md production run.
Thanks,
Kohamed
On Wed, May 6, 2020 at 10:40 Arun Srikanth wrote:
> Is it an NPT simulation or NVT simulation?
> Arun
>
> On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal,
> wrote:
>
> > Yes I measured both, the density and the free volume using
Is it an NPT simulation or NVT simulation?
Arun
On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal,
wrote:
> Yes I measured both, the density and the free volume using gromacs.
>
> Since the free volume changes with respect to time, shouldn’t the density
> also change with time ?
>
> Thanks,
>
Yes I measured both, the density and the free volume using gromacs.
Since the free volume changes with respect to time, shouldn’t the density
also change with time ?
Thanks,
Mohamed
On Wed, May 6, 2020 at 08:23 David van der Spoel
wrote:
> Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal:
> >
Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal:
Hello everybody,
I have two fundamental questions please.
I have measured the fee volume and I discovered that, the free volume
changes with respect to the time during the production run (different value
for each frame). However I have measured
I am simulating Crystal System (C60 molecules)
Thanks,
Mohamed
On Wed, May 6, 2020 at 1:22 AM Arun Srikanth wrote:
> Are you simulating a crystal or amorphous system?
>
> Arun
>
> On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal
> wrote:
>
> > Hello everybody,
> >
> > I have two fundamental
Are you simulating a crystal or amorphous system?
Arun
On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal
wrote:
> Hello everybody,
>
> I have two fundamental questions please.
>
> I have measured the fee volume and I discovered that, the free volume
> changes with respect to the time during the
Hello everybody,
I have two fundamental questions please.
I have measured the fee volume and I discovered that, the free volume
changes with respect to the time during the production run (different value
for each frame). However I have measured the density but the result does
not change with
Thank you Justin, you are a life saver..!
It's working now. You have correctly pointed out the issue.
Thank you so much.. :)
Regards,
Debashish
On Wed, May 6, 2020 at 12:11 AM Justin Lemkul wrote:
>
>
> On 5/5/20 5:54 PM, Debashish Banerjee wrote:
> > Dear gmx users,
> >
> > I have
On 5/5/20 5:54 PM, Debashish Banerjee wrote:
Dear gmx users,
I have been stuck in a problem for a month now and have scrutinized all the
past discussions and forms related to it dating as back as 9 years. Now I
really need your help.
My system has Clays (layered philosillacates), Cesium ions
Just a small rectification: *posres_Cs.itp* were created and used every
time. I mistakenly wrote posre_Cs.itp while typing it here, my bad.
Thanks,
Debashish
On Tue, May 5, 2020 at 11:54 PM Debashish Banerjee
wrote:
> Dear gmx users,
>
> I have been stuck in a problem for a month now and have
Dear gmx users,
I have been stuck in a problem for a month now and have scrutinized all the
past discussions and forms related to it dating as back as 9 years. Now I
really need your help.
My system has Clays (layered philosillacates), Cesium ions (Cs), acetate
molecules as well as water. In
On 5/5/20 12:12 PM, Neena Susan Eappen wrote:
Thank you Sahil, I will try VMD plugin for H-bond analysis.
Thank you Justin for your reply, it looks like gmx hbond considers only one N-H
as donor when part of NH2 group. Please take a look at this file.
This is what gmx hbond does by default,
On 5/4/20 11:46 PM, azadeh kordzadeh wrote:
Hi
Thank you very much for your answer to my former question
I want to select CYSH state but we have this option for this amino acid.
already I could determine especial state for his,lys,arg,asp by command -his
but this command doesn't work for CYS
On 5/2/20 3:12 PM, lazaro monteserin wrote:
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files:
I followed the protocol in gromacs website to do dihedral Principal
Component Analysis:
1) Created an index file (*dangle.ndx*) with a list of the dihedrals to
analyze
Thank you Sahil, I will try VMD plugin for H-bond analysis.
Thank you Justin for your reply, it looks like gmx hbond considers only one N-H
as donor when part of NH2 group. Please take a look at this file.
https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing
Many
Hi All,
I am simulating systems with lipids, water and surfactants. I observed
formation of water pools/water aggregates with different sizes in final
frames. Now I want to measure size of these pools. What gromacs tool do you
suggest me to use?
I tried to do clustering first and thought
Hi,
Have you tried reducing the timestep in mdp?
Yes, I tried. But no hope.
On Mon, May 4, 2020, 2:52 AM Naba https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
wrote:
>* Dear users and developers,
*>>* I have spent extensive amount of time to model glycosylated ASN residues
Hi
Thank you very much for your answer to my former question
I want to select CYSH state but we have this option for this amino acid.
already I could determine especial state for his,lys,arg,asp by command -his
but this command doesn't work for CYS
Thanks
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Gromacs Users mailing list
* Please
1/ it means that between the original coordinate file loaded with vmd and
the frame you are looking at there from the trajectory file, those atoms
have moved across the periodic boundary and vmd is still drawing the bond
between them. vmd knows nothing about bonds, it guesses where the bonds
Hi Jochen,
Thank you for the suggestions.
Best,
Zheng
On Mon, May 4, 2020 at 5:24 PM Jochen Hub
wrote:
>
>
> Am 04.05.20 um 23:21 schrieb Jochen Hub:
> >
> >
> > Am 04.05.20 um 21:33 schrieb Zheng Ruan:
> >> Hi,
> >>
> >> I'm trying to setup an antiparallel membrane system for CompEL
> >>
Am 04.05.20 um 23:21 schrieb Jochen Hub:
Am 04.05.20 um 21:33 schrieb Zheng Ruan:
Hi,
I'm trying to setup an antiparallel membrane system for CompEL
simulation.
It is relatively straightforward to convert an existing single membrane
system to a parallel system by using
# gmx genconf -f
Am 04.05.20 um 21:33 schrieb Zheng Ruan:
Hi,
I'm trying to setup an antiparallel membrane system for CompEL simulation.
It is relatively straightforward to convert an existing single membrane
system to a parallel system by using
# gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro
Hi,
I'm trying to setup an antiparallel membrane system for CompEL simulation.
It is relatively straightforward to convert an existing single membrane
system to a parallel system by using
# gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro
However, is there an easy way to invert one
Hello again @ all gmx-users!
A month has passed and we have moved forward with our work to move the
user mailing list to the [discussion forum]
https://gromacs.bioexcel.eu/. The discussion forum will open Friday, 8
May 2020.
We are now ready to accept people signing up to the forum at
Dear Gromacs users
I am doing free energy calculation of the protein-ligand system in gromacs
2020 in which I am annihilating ligand by removing charges and vdw
interactions. During Vdw removal I am facing lincs warning and my system
crashes by generating different pdb structures. I have tried to
I have done simulation water in nanopore based on quartz (I use model
ClayFF) using Gromacs 5.1.5 and have observed strange behavior. (Here is
a link to the pictures at the initial time (1.png) and in the modeling
process.
Hi Dinesh and others,
I see a few PLUMED tutorials available online, but I wanted to just let
anyone know that if they have developed a PLUMED tutorial or are working to
create a new one, please feel free to submit any high-quality tutorials to
LiveCoMS Journal:
https://www.livecomsjournal.org/
Dear gmx users,I am trying to run a protein-ligand simulation using PLUMED
patch.I would like to know if there is a step-by-step tutorial that could help
run metadynamics simulations using PLUMED (like the Gromacs tutorials already
available)
Dinesh Kumar
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*
Hi,
Do check out gmx do_dssp -h and make sure your dssp binary is the right
version, with executable permissions, in the right place (or alternatively
the appropriate environment variable is set, so that do_dssp can find dssp)
Mark
On Fri, 1 May 2020 at 18:47, Iman Katouzian wrote:
> Good
Dear users,
I have a corrupted .xtc file.
I can read only part of the whole frame in VMD.
When I gmx check the .edr file, there is no problem with 5001 frames.
However if I do gmx check the .xtc file, then I get only 2954 frames out of
50001 frames.
I used Gromacs 2019.6 with CUDA on a single
OPLS tends to be a common choice for graphene. That being said, if you really
want to use gromos (for some reason), be sure (as Alex has stated) to make sure
that the graphene edges match across the PBC otherwise do not use PBC (but then
be sure to change your electrostatics appropriately and
How did you set up your graphene sheet originally? Also are you treating the
sheet as an infinite sheet (using with periodic molecules)?
-Micholas
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Mohamed
Abdelaal
Sent: Sunday, May 3, 2020 8:40
Protonation state of the amino acids are set during execution of pdb2gmx and
you can choose yourself what their protonation state is using -inter or any
of the other options if you don't want to go through all.
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html
Catch ya,
You have pressure scaling and LINCS convergence issues, suggesting that
the starting configuration is far from equilibrium, as well as
potentially other issues.
Gromos FF is not appropriate for graphene, and neither is turning C-C
bonds into LINCS constraints, as set by your 'all-bonds' --
Hello everyone,
I am simulating the evaporation of non protein molecules on a graphene
sheet. I am using gromos force field and hence the lincs constrain are set
to all-bonds. I have done the energy minimization and NVT
successfully without any warnings. During the NPT equilibiration I got
Hi,
Have you tried reducing the timestep in mdp?
On Mon, May 4, 2020, 2:52 AM Naba wrote:
> Dear users and developers,
>
> I have spent extensive amount of time to model glycosylated ASN residues
> covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein using
> Amber99SB-ILDN
Dear Gromacs users;
I have generated Gibbs free energy landscapes from the two first principal
components PC1 and PC2 obtained from Dihedral Principal Component analysis
performed using Gromacs.
So, now I have a file *"shamlog-1_2.log" *that contain a list of the bins
ordered by energy, for
Dear users and developers,
I have spent extensive amount of time to model glycosylated ASN residues
covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein using
Amber99SB-ILDN force field. Though there may be easy way to do this
with CHARMM-GUI, I want it for Amber force field for
Hi
I gave a topology of a protein with pdb2gmx command in next step I change
protonation some aminoacids but the topology didn't chage. How could I
create new topology?
I need to obtain topology protonated aminoacid from other servers?
Thanks
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Gromacs Users mailing list
* Please search the
gmx distance -oxyz ?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every
Thank you very much, Justin, for your valuable feedback.
Regards.
Sadaf
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* For
Dear Gromacs users
I am using amber99sb-ildn.ff force field for protein and I used GAFF for
ligand parameterization.
I tried different options e.g using constraint =all bonds as well as
h-bonds. Reducing the time step to 1 fs but still, I could not solve the
problem and get lincs warning
Hi Nikhil,
Lazaro Andres Monteserin Castanedo (lamonteserincastan...@gmail.com) invited
you to edit the folder " dPCA " on Dropbox.
Lazaro Andres said:
"Dear Dr. Lemkul I used the following protocol to generate the (.xpm)
filesI followed the protocol in gromacs website to do dihedral
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files:
I followed the protocol in gromacs website to do dihedral Principal
Component Analysis:
1) Created an index file (*dangle.ndx*) with a list of the dihedrals to
analyze from my molecule. I wrote this file in a text editor
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files:
I followed the protocol in gromacs website to do dihedral Principal
Component Analysis:
1) Created an index file (*dangle.ndx*) with a list of the dihedrals to
analyze from my molecule. I wrote this file in a text editor
Hello all,
I was trying to install GROMACS 2020.2 and encountered a failed test at make
check (#43, mdrun). I pasted what I think is the pertinent snippet below and
the full output is in the link:
https://www.dropbox.com/s/nfq6yojjdslhxur/make_check.log?dl=0
The cmake incovation was: cmake ..
On 5/2/20 12:13 PM, Eugene Radchenko wrote:
Hello,
I wanted to report a bug using the Redmine site.
Unfortunately, even after registering, the option to submit an issue is missing
from the Issues page (where I expected it).
While the “File a new issue” link from the main page to
Hello,
I wanted to report a bug using the Redmine site.
Unfortunately, even after registering, the option to submit an issue is missing
from the Issues page (where I expected it).
While the “File a new issue” link from the main page to
https://redmine.gromacs.org/projects/gromacs/issues/new
Oh thank you so much, I did not know it was a reference value. Given a
range of values might exist in one system I'm guessing minimization would
be the only way to deal with such a situation.
Best, Miro
On Sat, May 2, 2020 at 9:53 PM Justin Lemkul wrote:
>
>
> On 5/2/20 6:54 AM, Miro Astore
On 5/2/20 8:21 AM, Sadaf Rani wrote:
Dear Justin
I want to get the equilibrium value for bond, angle and dihedral restraints
to use in free energy calculation as mentioned in:-
https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467
Looking forward to your kind suggestions, please.
You can
Dear Justin
I want to get the equilibrium value for bond, angle and dihedral restraints
to use in free energy calculation as mentioned in:-
https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467
Looking forward to your kind suggestions, please.
Thanks.
Sadaf
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On 5/2/20 6:54 AM, Miro Astore wrote:
Hi all,
I'm trying to make a protein with a fair few disulfide bridges and I
couldn't get it to work. I chose -ss yes and increased the minimum distance
in specbonds.dat but it doesn't seem to want to let me see all possible
pariings.
specbond.dat does
On 5/1/20 2:41 PM, Sadaf Rani wrote:
Dear Gromacs users
I did 50ns MD simulation of a protein-ligand complex. From this trajectory,
I extracted region of trajectory having stable rmsd and generated an
average structure. I want to run this average structure to get an idea of
setting some
On 5/1/20 9:29 AM, John Whittaker wrote:
Hi Mohamed,
Hello everybody,
In order to solve the PBC at the end I use the command:
*gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *
followed by:
*gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb*
I want to solve
On 4/30/20 2:07 PM, lazaro monteserin wrote:
Dear Dr. Lemkul I did it. It works. Thank you very much for the advise.
Now I am having issues opening the (.xpm) files generated that contain for
example the gibbs energy landscape on the two first eigenvectors of the
dPCA.
If I use the command
Hi all,
I'm trying to make a protein with a fair few disulfide bridges and I
couldn't get it to work. I chose -ss yes and increased the minimum distance
in specbonds.dat but it doesn't seem to want to let me see all possible
pariings.
Any way I can nudge it in the right direction without
Dear Gromacs users
I did 50ns MD simulation of a protein-ligand complex. From this trajectory,
I extracted region of trajectory having stable rmsd and generated an
average structure. I want to run this average structure to get an idea of
setting some restraints. but when I do gmx pdb2gmx I get
Good day,
I have recently downloaded the latest dssp version and with the mkdssp
executable file as I type chmod +x dssp and run this code :
gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg
-tu ns
the process starts but no output is created after even 1 day
my
Hi Mohamed,
> Hello everybody,
>
> In order to solve the PBC at the end I use the command:
>
> *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *
>
> followed by:
>
> *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb*
>
>
> I want to solve this problem after the energy
Dear all,
I like to calculate the conformation tensor for a mass of a short polymer.
The conformation tensor is defined as c_ij = 3* ( /
<(Re_bulk)^2>), in which Re_i and Re_j are the Cartesian components of the
Re as the end-to-end vector. Several gmx options are available to calculate
the
Hello everybody,
In order to solve the PBC at the end I use the command:
*gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *
followed by:
*gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb*
I want to solve this problem after the energy minimization but I don't have
Dear Dr. Lemkul I did it. It works. Thank you very much for the advise.
Now I am having issues opening the (.xpm) files generated that contain for
example the gibbs energy landscape on the two first eigenvectors of the
dPCA.
If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o
Hi GROMACS users,
The official release of GROMACS 2020.2 is available!
This second patch release again fixes issues found since the initial
release of GROMACS 2020 and the release of 2020.1. We encourage all
users of the 2020
series to update to 2020.2. Please see the link to the release
On 4/30/20 7:10 AM, Sadaf Rani wrote:
Dear Justin
I have removed the blank lines but getting a new warning while doing gmx
pdb2gmx:-
WARNING: Duplicate line found in or between hackblock and rtp entries
I am not getting what else is wrong. Could you please help me to figure out.
I have
Dear Justin
I have removed the blank lines but getting a new warning while doing gmx
pdb2gmx:-
WARNING: Duplicate line found in or between hackblock and rtp entries
I am not getting what else is wrong. Could you please help me to figure out.
I have shared the file on the following link:-
On 4/29/20 7:41 PM, Sadaf Rani wrote:
Dear Justin
I have shared the files for the users mailing list on the following link.
https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0
Remove the blank lines from the end of atomtypes.atp and it works fine.
Note that you
On 4/29/20 7:11 PM, lazaro monteserin wrote:
Dear Dr. Lemkul it could be possible use that angle.index with the selected
dihedrals written by hand as index file for gmx angle for dihedral
Principal Component Analysis?
You can create index groups however you like for whatever analysis you
Dear Justin
I have shared the files for the users mailing list on the following link.
https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0
Thanks and Regards.
Sadaf
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Dear Dr. Lemkul it could be possible use that angle.index with the selected
dihedrals written by hand as index file for gmx angle for dihedral
Principal Component Analysis? Kindly,
Lazaro
On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote:
>
>
> On 4/29/20
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