On 10/25/13 11:32 AM, Sajad Ahrari wrote:
thanks for replying. are these features available under Gromacs? and is there
any tutorial or related material I can grasp to stand up for start?
My umbrella sampling tutorial covers generating a PMF. MM/PBSA is just a
post-processing technique,
On 10/25/13 11:43 AM, Sajad Ahrari wrote:
is AMBER facilities the only way of approaching MM-PBSA calculations? could you
lead me to any other software more friendly with Gromacs MD output?
See what Google tells you.
-Justin
--
==
Justin A.
Hi,
You can email me we have a tool for mmpbsa with gromacs
Andrea
Messaggio inviato dal mio ASUS MeMO Pad
Justin Lemkul jalem...@vt.edu ha scritto:
On 10/25/13 11:43 AM, Sajad Ahrari wrote:
is AMBER facilities the only way of approaching MM-PBSA calculations? could
you
lead me to any
Hi, all-
At this point, any fixes are going to be in the 5.0 version, where the
integrators will be a bit different. If you upload your system files
to redmine.gromacs.org (not just the .mdp), then I will make sure this
gets tested there.
On Fri, Oct 25, 2013 at 10:14 AM, Guillaume Chevrot
Dear jkrieger
I used 2 times trjconv tool:
1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump
2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center
Dear Mark
I selected all lipid atoms for centering.
With my manner, pbc problem was solved just for
dear users,
I am performing 500ps mdrun in vacuum for polypeptide(formed
by 10-residues leucine) using gromacs_4.5.5(double-precision) using
opls-aa/L force field.Input file for 500ps mdrun is given below
title= peptide in vaccum
cpp=
Hi,
can one output how mdrun threads are pinned to CPU cores?
Thanks,
Carsten
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please
Dear all,
I want to use the Gromos54A8 FF in gromacs. They are available in gromos
format in http://www.gromos.net/main.pl ATB is yet to release it in
gromacs format.
I want to undertake the conversion of this FF to gromacs format. Apart from
On Oct 24, 2013 8:10 AM, shahab shariati shahab.shari...@gmail.com
wrote:
Dear jkrieger
I used 2 times trjconv tool:
1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump
2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol
-center
Dear Mark
I selected
Not working is too vague a symptom for anyone to guess what the problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote:
dear users,
I am performing 500ps mdrun in vacuum for polypeptide(formed
by 10-residues leucine) using
On 10/24/13 1:03 AM, JuYeon wrote:
dear gromacs users
im using gromacs to make CS2 MD programs i made pdb file (by converting mol
file to pdb file) and rtp file for CS2this is what i made
pdb file
COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.2HETATM1 C LIG
1 19.882
On 10/24/13 6:43 AM, rajat desikan wrote:
Dear all,
I want to use the Gromos54A8 FF in gromacs. They are available in gromos
format in http://www.gromos.net/main.pl ATB is yet to release it in
gromacs format.
I want to undertake the conversion of this FF to gromacs format. Apart from
Hi Justin,
Thanks for the comments.
Since the script was written in 2009, I don't want to use it until I verify
that the formats are unchanged.
The same would apply here - if you want to validate between the two
software packages, carry out equivalent calculations in both programs.
I didn't
On 10/24/13 9:00 AM, rajat desikan wrote:
Hi Justin,
Thanks for the comments.
Since the script was written in 2009, I don't want to use it until I verify
that the formats are unchanged.
I doubt there have been any significant changes.
The same would apply here - if you want to validate
Thanks Justin!
If I manage to port it, I will share in the user contributions.
Regards,
On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/24/13 9:00 AM, rajat desikan wrote:
Hi Justin,
Thanks for the comments.
Since the script was written in 2009, I don't want
Hi,
I have been trying to add ions to my system so as to make it neutral.
However, I always obtain the same result:
Solvent Group size (950) is not multiple of 9.
The command I entered in this step was:
genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+
-nname CL-
How
On 10/24/13 9:34 AM, felipe vasquez wrote:
Hi,
I have been trying to add ions to my system so as to make it neutral.
However, I always obtain the same result:
Solvent Group size (950) is not multiple of 9.
What group did you choose at the genion prompt?
The command I entered in this
Hi,
I chose group 0 (System), but I also tried others like 1 (Protein) or 2
(Protein+H) with the same result.
Regards,
Andrés F.
*Andrés Felipe Vásquez J., MSc.*
Grupo de Fisiología Molecular
Subdirección de Investigación Científica y Tecnológica
Dirección de Investigación en Salud Pública
On 10/24/13 10:21 AM, felipe vasquez wrote:
Hi,
I chose group 0 (System), but I also tried others like 1 (Protein) or 2
(Protein+H) with the same result.
You don't want to embed ions into your protein or haphazardly into the system.
You'll start deleting random segments of molecules, or
Hi,
No. mdrun reports the stride with which it moves over the logical cores
reported by the OS, setting the affinity of GROMACS threads to logical
cores, and warnings are written for various wrong-looking cases, but we
haven't taken the time to write a sane report of how GROMACS logical
threads
On Oct 24, 2013, at 4:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi,
No. mdrun reports the stride with which it moves over the logical cores
reported by the OS, setting the affinity of GROMACS threads to logical
cores, and warnings are written for various wrong-looking cases, but
Dear Mark
Thank for your reply.
If I show my system as 4 regions, my system before equilibration is as fallows:
region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water
After equilibration, drug molecule exits region (1) and enters
On 10/24/13 10:57 AM, shahab shariati wrote:
Dear Mark
Thank for your reply.
If I show my system as 4 regions, my system before equilibration is as fallows:
region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water
After
Hi there,
I am using gromacs-4.6.1 with this mdp file:
integrator = md; leap-frog integrator
nsteps = 300 ; 6.0 ns
dt = 0.002 ; 2 fs
nstxout = 0 ; save coordinates every 10 ps
nstvout = 0 ; save
I think nstcalclr would only do something if you have longer range
interactions to calculate (lr means longer than rlist). Therefore
something has be longer than rlist for this to happen.
Hi there,
I am using gromacs-4.6.1 with this mdp file:
integrator= md; leap-frog
Thanks Justin for the quick hint!
So, only the last two columns are needed. Sorry for the stupid question,
where can I obtain reliable values for the atomic van der waals radii? Is
it I have to calculate from the original force field parameters, in my
case, the opls?
Corina
On Fri, Oct 25, 2013
Dear Gromacs users,
I am interested to do implicit solvent MD but I find that some atoms
(atomtype opls_961-965) in my system does not have parameters in the file
gbsa.itp.
Does anyone know the meaning of these columns in the file and the proper way
to derive these values?
; atypesarst
On 10/24/13 12:02 PM, Corina Mo wrote:
Dear Gromacs users,
I am interested to do implicit solvent MD but I find that some atoms
(atomtype opls_961-965) in my system does not have parameters in the file
gbsa.itp.
Does anyone know the meaning of these columns in the file and the proper way
to
On 10/24/13 12:11 PM, Coco Mo wrote:
Thanks Justin for the quick hint!
So, only the last two columns are needed. Sorry for the stupid question,
where can I obtain reliable values for the atomic van der waals radii? Is
it I have to calculate from the original force field parameters, in my
case,
On Thu, Oct 24, 2013 at 4:52 PM, Carsten Kutzner ckut...@gwdg.de wrote:
On Oct 24, 2013, at 4:25 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
No. mdrun reports the stride with which it moves over the logical cores
reported by the OS, setting the affinity of GROMACS threads to
Ja. No twin-range = no long-range :-)
Mark
On Thu, Oct 24, 2013 at 5:50 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
I think nstcalclr would only do something if you have longer range
interactions to calculate (lr means longer than rlist). Therefore
something has be longer than rlist for this to
Dear Justin,
Thanks again! Will look into it.
Btw, you know if there is any plan to implement implicit lipid model in
GROMACS?
Corina
On Fri, Oct 25, 2013 at 12:17 AM, Justin Lemkul [via GROMACS]
ml-node+s5086n5011968...@n6.nabble.com wrote:
On 10/24/13 12:11 PM, Coco Mo wrote:
Thanks
As Justin said, there is no actual division between region 1 and 4.
Apparently you got the free diffusion you asked for! :-)
Mark
On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati
shahab.shari...@gmail.comwrote:
Dear Mark
Thank for your reply.
If I show my system as 4 regions, my system
Hi Carsten,
On Thu, Oct 24, 2013 at 4:52 PM, Carsten Kutzner ckut...@gwdg.de wrote:
On Oct 24, 2013, at 4:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi,
No. mdrun reports the stride with which it moves over the logical cores
reported by the OS, setting the affinity of GROMACS
Hi
I would like to try it out
Srinivasa Rao Penumutchu
Research Scholar
Protein NMR Lab , II floor-218
Department of Chemistry
National Tsing Hua University,
Hsinchu, Taiwan.
Ph: 886357151-35605,
Email- penumutchu.srini...@gmail.com ,s9923...@m99.nthu.edu.tw
--
View this message in
Your restraint involving group C should use pull_group2, etc, not another copy
of pull_group1. Other than that,
it looks like a valid approach.
Chris.
-- original message --
I am going to perform the two-dimensional umbrella sampling using a pair of
distances (the distance btw atoms A and
Dear Kevin,
I'm Gloria Saracino from the Center of Nanomedicine and Tissue Engineering of
the Hospital of Niguarda Ca' Granda in Milan, Italy.
I'm interested into knowing more about this new web based toolas I use MD
everyday.
Let me know what I have to do.
Regards,
Gloria Saracino
On Oct 23, 2013 7:24 AM, rajat desikan rajatdesi...@gmail.com wrote:
Hi,
We recently had a software upgrade in our cluster from gromacs 4.5.4. to
gromacs 4.6.3.. I need to continue an earlier simulation that had been run
in 4.5.4. using the .cpt, .tpr and .mdp.
Are there any issues with
On Oct 23, 2013 5:34 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
I am running a NPT simulation for cyclopropylchloride(1) in
50%water(100)+50%ethanol(100) using opls force field parameter .
After equilibration box size increases from 20 A to 70 A.
Really? Seems wildly unlikely
If the job is not very parallel, it will not crash.
It is better to preequilibrate in NVT beforehand. Cyclopropylchloride
is probably a liquid at 290K, if the model is parametrized reasonably.
So it should not phase-separate.
Vitaly
On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham
By crash I meant explode not DD is impossible. Explosions don't
happen because of parallelism, they happen because the steps are too large
for the size of the forces. The forces required to stably expand a box from
20A to 70A seem likely to be so large that I am very skeptical that you
could
I also would like to try
2013/10/23 Gloria Saracino glos...@yahoo.it
Dear Kevin,
I'm Gloria Saracino from the Center of Nanomedicine and Tissue Engineering
of the Hospital of Niguarda Ca' Granda in Milan, Italy.
I'm interested into knowing more about this new web based toolas I use MD
Hi all,
I have never performed TFE-water simulation therfore I want to know after
inserting the peptide in the pre-equilibrated TFE-water mixture, do we need
to adjust the number of TFE or water molecules ?
or should I directly add ions to this system and run the production run.
Any suggestion
Thank you, Mark!
On Wed, Oct 23, 2013 at 2:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Oct 23, 2013 7:24 AM, rajat desikan rajatdesi...@gmail.com wrote:
Hi,
We recently had a software upgrade in our cluster from gromacs 4.5.4. to
gromacs 4.6.3.. I need to continue an
On 10/22/13 9:57 PM, Nimmy McNimmerson wrote:
I have some simulations of inserting a probe molecule into a bilayer. Some
molecules work fine. However, a certain class of molecules is taking an
absurdly long time to run the exact same simulation, even though I energy
minimized the molecules
On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote:
Hi all,
I have never performed TFE-water simulation therfore I want to know after
inserting the peptide in the pre-equilibrated TFE-water mixture, do we need
to adjust the number of TFE or water molecules ?
That depends on how you
me to
On Wed, Oct 23, 2013 at 12:27 PM, Thales Kronenberger
kronenberg...@gmail.com wrote:
I also would like to try
2013/10/23 Gloria Saracino glos...@yahoo.it
Dear Kevin,
I'm Gloria Saracino from the Center of Nanomedicine and Tissue
Engineering
of the Hospital of
There shouldn't be a problem for that. BTW, can you also enter a ticket at
Daigrid.org for this matter?
Thanks
-Kevin
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of rajat desikan
Sent: Wednesday, October 23, 2013 1:24 AM
To:
Hi,
Sounds very interesting. Can I have a test account, please?
The Lindahl group has some related work going on at
http://copernicus-computing.org/, automating large-scale simulation
workflows. I'm not sure yet whether we have any synergies! :-)
Cheers,
Mark
On Tue, Oct 22, 2013 at 4:34 PM,
Hi Kevin,
It seems interesting. I would like to try it out. May I have an account?
Best regards,
Ehsan
- Original Message -
From: Kevin Chen fch6...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, October 22, 2013 7:34:10 AM
Subject: [gmx-users] a
Please could I have an account too.
Hi Everyone,
I'm writing to let you guys know that we have developed a web-based tool
MD
simulation tool for GROMACS. It is a software package primarily developed
for biological MD and offers a huge amount of possible options and
settings
for tailoring
I'd like to check it out too
On Wed, Oct 23, 2013 at 8:45 AM, Ehsan Sadeghi es...@sfu.ca wrote:
Hi Kevin,
It seems interesting. I would like to try it out. May I have an account?
Best regards,
Ehsan
- Original Message -
From: Kevin Chen fch6...@gmail.com
To: Discussion list
Dear gromacs users
My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
rectangular box.
I put drug molecule in 2 position: a) drug in the center of bilayer
membrane, b) drug inside water molecules in top leaflet.
For both positions, I did energy minimization successfully with
Hi Kevin
I would like to try it out.. Let me know the procedure to create an
account..
Regards
Ash
On Tuesday, October 22, 2013, Kevin Chen wrote:
Hi Everyone,
I'm writing to let you guys know that we have developed a web-based tool MD
simulation tool for GROMACS. It is a software package
Sound nice. I would like to try out.
Could You please set up an account for me?
Regards,
Eduardo Villarreal
villarea...@hss.edu
-
Eduardo Villarreal Ramírez
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.
--
View this
Hi Kevin
Can I have a try?
Best
Houyang
On Wed, Oct 23, 2013 at 12:30 PM, Villarealed villarea...@hss.edu wrote:
Sound nice. I would like to try out.
Could You please set up an account for me?
Regards,
Eduardo Villarreal
villarea...@hss.edu
-
Eduardo Villarreal Ramírez
Postdoctoral
Sorry, i should want to be delete my contact from mailing list.
thanks
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post
On 10/23/13 12:44 PM, Michelangelo Scordino wrote:
Sorry, i should want to be delete my contact from mailing list.
thanks
Unsubscribing is explained in the footer of every email that hits the list:
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to
I ran into this, you basically should determine your time frame, and install 4.5.4 if its a problem local (only 1-2 hours), to finish the work, otherwise you need to start from scratch. But I did this with older versions, so do not know about higher versions (such as if theprogrammerseliminated
I usually use -pbc nojump for my protein simulations and this works every
time.
Dear gromacs users
My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
rectangular box.
I put drug molecule in 2 position: a) drug in the center of bilayer
membrane, b) drug inside water
Center on a particular lipid? Or head group?
Mark
On Oct 23, 2013 6:13 PM, shahab shariati shahab.shari...@gmail.com
wrote:
Dear gromacs users
My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
rectangular box.
I put drug molecule in 2 position: a) drug in the center of
Hello,
I am trying to convert a protein+ATP+water+ion system pdb into gromacs
files. I need to use the existing water and ion coordinates. I can
convert the protein part using pdb2gmx and grompp fine. But, I do not know
how to process the solvent and ion coordinates separately and combine them
On 10/23/13 4:28 PM, Dina Mirijanian wrote:
Hello,
I am trying to convert a protein+ATP+water+ion system pdb into gromacs
files. I need to use the existing water and ion coordinates. I can
convert the protein part using pdb2gmx and grompp fine. But, I do not know
how to process the solvent
got it. Thanks Justin.
On Wed, Oct 23, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/23/13 4:28 PM, Dina Mirijanian wrote:
Hello,
I am trying to convert a protein+ATP+water+ion system pdb into gromacs
files. I need to use the existing water and ion coordinates. I can
Hi,
I also want to try :)
Best regards,
~Thu
On Wed, Oct 23, 2013 at 11:39 PM, houyang chen houyangc...@gmail.comwrote:
Hi Kevin
Can I have a try?
Best
Houyang
On Wed, Oct 23, 2013 at 12:30 PM, Villarealed villarea...@hss.edu wrote:
Sound nice. I would like to try out.
Could You
dear gromacs users
im using gromacs to make CS2 MD programs i made pdb file (by converting mol
file to pdb file) and rtp file for CS2this is what i made
pdb file
COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.2HETATM1 C LIG
1 19.882 -4.263 -0.027 1.00 0.00 C
The sum of the two largest charge group radii (13.336) is larger
than rlist(1.2) - rvdw/rcoulomb i am getting this error while running
membrane simulations. please any one suggest how to rectify this error.
--
regards
M.SathishKumar
--
gmx-users mailing listgmx-users@gromacs.org
Probably, make your broken molecules whole before passing them to grompp.
Mark
On Tue, Oct 22, 2013 at 8:26 AM, Sathish Kumar sathishk...@gmail.comwrote:
The sum of the two largest charge group radii (13.336) is larger
than rlist(1.2) - rvdw/rcoulomb i am getting this error while running
Dear all users
I have simulated a protein with two chains (153 residues each) for
50ns(restarting crashed run 3 times) using a cubic box with each side as
11nm. After finding the closest distance between the periodic images, I
found that the closest distance becomes lesser than 1 after 23ns for
Hi Nidhi,
These are periodicity artifacts. Make sure that you remove jumps over PBC
from your trajectory by using trjconv -pbc nojump.
Cheers,
Tsjerk
On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal nidhikatyal1...@gmail.comwrote:
Dear all users
I have simulated a protein with two chains
Dear Sir,
I am doing fullerene interaction with DMPC , i downloaded
the gro file from the website mentioned in the tutorial. I was keep the
fullerene on the top of DMPC. But in the gro file already water is present.
If i removed that water molecules and adding new water
Thank you sir.
On Tue, Oct 22, 2013 at 2:48 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Nidhi,
These are periodicity artifacts. Make sure that you remove jumps over PBC
from your trajectory by using trjconv -pbc nojump.
Cheers,
Tsjerk
On Tue, Oct 22, 2013 at 11:14 AM, Nidhi
Hi Everyone,
I'm writing to let you guys know that we have developed a web-based tool MD
simulation tool for GROMACS. It is a software package primarily developed
for biological MD and offers a huge amount of possible options and settings
for tailoring the simulations. Seamlessly integrated with
Is there a link to the documentation? It's a little difficult to know
exactly what this supposed to be doing. Is it a GUI interface to
gromacs?
In general, it would be great to get these sort of extensions
coordinated with the main gromacs development tree, since otherwise
they would tend to
Dear all,
I have some doubt for the output force. What contributions do the output
forces in .trr file include? Certainly, the pair forces and bonded
interactions are included. However, if the external field (such as electric
field) is applied, is the external force included? In addition, if the
Hi Michael,
Sorry, if this is not the right place to post message of such. To answer
your question, it is a web-based GUI interface to GROMACS, which is a
perfect fit for those who are trying to learn MD or to run large scale
protein simulations on HPC.
Best Regards,
KevinFeng Chen, Ph.D.
On 10/22/13 9:15 AM, Sathish Kumar wrote:
Dear Sir,
I am doing fullerene interaction with DMPC , i downloaded
the gro file from the website mentioned in the tutorial. I was keep the
fullerene on the top of DMPC. But in the gro file already water is present.
If i removed
Hi Everyone,
I am having an awkward situation. I want to use g_density to get the
density profile of a lipid bilayer. At first glance, it looks like a
trivial task. But for my case, it's not because I have conflicting atom
names from two different molecules. I am using GROMOS 53a6. In DPPC
On 10/22/13 9:05 PM, Bin Liu wrote:
Hi Everyone,
I am having an awkward situation. I want to use g_density to get the
density profile of a lipid bilayer. At first glance, it looks like a
trivial task. But for my case, it's not because I have conflicting atom
names from two different
Hi!
It is strange but such combination works:
CC=icc CXX=icpc ~/cmake-2.8.12/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/ifs/apps/GROMACS-4.6.3 -DGMX_X11=OFF
-DGMX_MPI=ON -DGMX_FFT_LIBRARY=mkl -DGMX_GPU=ON cmake.log
It was a command that our cluster administrator was able to configure
GROMACS
I have some simulations of inserting a probe molecule into a bilayer. Some
molecules work fine. However, a certain class of molecules is taking an
absurdly long time to run the exact same simulation, even though I energy
minimized the molecules individually beforehand and there are no overlaps.
Hello,
I am running a NPT simulation for cyclopropylchloride(1) in
50%water(100)+50%ethanol(100) using opls force field parameter .
After equilibration box size increases from 20 A to 70 A.
I used the following mdp file.
; RUN CONTROL PARAMETERS =
integrator = sd
; start time and
It depending the time steps that u used or the molecule that u had is
big..Thats why ur EM take a long time..Is better take a long time
rather than quick but had a lot of errors..
On Wed, Oct 23, 2013 at 9:59 AM, Nimmy McNimmerson [via GROMACS]
ml-node+s5086n5011918...@n6.nabble.com wrote:
I
Hi,
We recently had a software upgrade in our cluster from gromacs 4.5.4. to
gromacs 4.6.3.. I need to continue an earlier simulation that had been run
in 4.5.4. using the .cpt, .tpr and .mdp.
Are there any issues with continuing these runs in 4.6.3.? Can I
concatenate these trajectories for
Dear Users,
I am doing protein-ligand MD simulations. I first prepare the ligand by
adding Hydrogen atoms and setting the charges using UCSF chimera. I
thereafter use acpype to get the ligand's gro,itp and top files. Finally, i
process the protein.PDB file and perform MD simulations. However, when
Dear users
I want to use some ions in my simulation (Phosphorus, Sulfur and ...).
How can I know in which FF these are present?
And what can I do if no FF include the interested Ions?
any suggestion is appreciated in advacne
Best
Mohsen
--
gmx-users mailing listgmx-users@gromacs.org
Have you tested your ligand alone in MD simulation and how vmd would show
it?
Alan
On 21 October 2013 08:31, MUSYOKA THOMMAS mutemibiochemis...@gmail.comwrote:
Dear Users,
I am doing protein-ligand MD simulations. I first prepare the ligand by
adding Hydrogen atoms and setting the charges
On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote:
Dear users
I want to use some ions in my simulation (Phosphorus, Sulfur and ...).
How can I know in which FF these are present?
Phosphorus and sulfur aren't ions. There are P and S atomtypes in most force
fields that are suitable for several
Sounds like issues with
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions,
strategies for coping found there.
Mark
On Mon, Oct 21, 2013 at 9:31 AM, MUSYOKA THOMMAS
mutemibiochemis...@gmail.com wrote:
Dear Users,
I am doing protein-ligand MD simulations. I first
Please keep the discussion on the gmx-users mailing list.
On 10/21/13 6:24 AM, sunyeping wrote:
Dear professor Lemkul,
Thank you for the reply. But I still have some questions about the umbrella
sampling tutorial. In setion 2 of the tutorial, define the unit cell, for the
command:
editconf
Dear Dr. Justin
Thank you for your reply
You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
ions.
I want to have these ions in my solution.
On Mon, Oct 21, 2013 at 1:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote:
Dear
On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote:
Dear Dr. Justin
Thank you for your reply
You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
ions.
I want to have these ions in my solution.
Many force fields include these ions or closely related model compounds. Have a
sure, thank you.
On Mon, Oct 21, 2013 at 4:49 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote:
Dear Dr. Justin
Thank you for your reply
You are right, I am sorry for my mistake. I meant Phosphate and Sulfate
ions.
I want to have these ions in
Dear all,
I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do
equilibration by GROMACS. I know GROMACS can build the system, but my
subsequent production run must be conducted by CHARMM. I want to use
GROMACS to do equilibration cuz it may take long to get it equilibrated.
On 10/21/13 11:14 AM, Zhi Yue wrote:
Dear all,
I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do
equilibration by GROMACS. I know GROMACS can build the system, but my
subsequent production run must be conducted by CHARMM. I want to use
GROMACS to do equilibration cuz
Hi Justin,
Thanks for your advice. I'll try again. Have a wonderful night!
Best
Shane
On Mon, Oct 21, 2013 at 6:51 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/21/13 11:14 AM, Zhi Yue wrote:
Dear all,
I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do
I have completed the simulations using couple-intramol = yes
Reminder, have a molecule that are calculating the Gibbs energy of hydration
and solvation (octanol). In one topology the only difference is the atomic
charges have been doubled. Considering that charges are scaled linearly with
Dear gromacs users,
I am studying gromacs umbralla sampling. I want to pull a lingand out of
its binding pocket in a protein. By observing the ligand-protein complex, I
think I should pull the ligand along a direction which is not parallel to the
x, y or z axis so as to prevent the ligand
On 10/20/13 9:13 AM, sunyeping wrote:
Dear gromacs users, I am studying gromacs umbralla sampling. I want to pull a
lingand out of its binding pocket in a protein. By observing the
ligand-protein complex, I think I should pull the ligand along a direction
which is not parallel to the x, y or z
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to
501 - 600 of 58539 matches
Mail list logo
