You need to contact your cluster administrator for instructions of how to
submit jobs to the cluster. Usually you have to create some kind of
shell-script that specifies various parameters of your job and then submit it
to a queue system.
Below you submitted the job most likely to the
Thanks for the reply Dr. Justin.
I have also thinking of the same possibility but to further confirm, I am
sending the link for the plot of the distance between the COM of ligand
binding pocket and COM of ligand molecule, please find some time to have a
look at the plot and let me know if it seems
On 10/7/13 1:39 PM, bipin singh wrote:
Thanks for the reply Dr. Justin.
I have also thinking of the same possibility but to further confirm, I am
sending the link for the plot of the distance between the COM of ligand
binding pocket and COM of ligand molecule, please find some time to have a
Hello Gromacs users,
I want to obtain the topology file (topol.top) for this peptide
Ace-Ser-Ser-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-NH2.
I am using this ffG43a1p force field and this command pdb2gmx -f sereno2.pdb
-o pep5-dpp-cap-linear-phospho_newbox_up_rotate.gro -ignh -ter
On 10/7/13 4:40 PM, Villarealed wrote:
Hello Gromacs users,
I want to obtain the topology file (topol.top) for this peptide
Ace-Ser-Ser-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-NH2.
I am using this ffG43a1p force field and this command pdb2gmx -f sereno2.pdb
-o
Dear Justin,
Your are right, as usual.
Thank you so much.
-
Eduardo Villarreal Ramírez
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.
--
View this message in context:
With a ligand diffusing as freely as I'm assuming (you've omitted a lot of
info, box size etc.) you aren't going to get PBC to play nice, although
-nojump should have atleast given you a different wrong answer.
Centering the system on the same point you are using to define the binding
pocket (may
Dear gmx-users,
I have just finished umbrella MD but I missed to type pullf/pullx options
on mdrun.
So, can I get pullf/pullx .xvg files from mdrun results?
Best regards,
Yoochan
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Dear All,
I am trying to follow lipid bilayer simulation tutorial,I am
getting struck at energy minimization same step after generating
system_inflated.gro file. I get the same error,
Fatal error:
Invalid line in system_inflated.gro for atom 6439:
25.67360 25.77400 6.59650
I
Thanks for the reply Dr. Trayder and Dr. Justin.
I have performed unrestrained MD with a ligand bound protein having surface
exposed binding pocket (link of the image attached for clarification). I
have used a cubic box with vectors 6.432nm and the system size was 4.117
3.878 and 4.059 (in nm).
Hi Chris,
The activation energy is obtained from the PMF well depth. So that leaves
two variables k and A. If we get K at say 5 temepratures, and plot ln(k)
vs. 1/T, the intercept will give us A. From that, at the temperature of
interest, we can back out k.
I will dig up the paper I saw this in.
On 10/6/13 12:47 AM, hasthi wrote:
Dear GROMACS users,
I have been trying to simulate protein of
my interest in lipid bilayer(POPC) . I am following the tutorial of KALP-15
in DPPC. When I try to minimise the system after generating
system_inflated.gro. I get a
Dear gromacs users
My system contains DOPC + CHOLESTEROLO + WATER in a rectangular box.
I did energy minimization successfully with following mdp file.
--
; Parameters describing what to do, when to stop and what
On 10/6/13 10:03 AM, shahab shariati wrote:
Dear gromacs users
My system contains DOPC + CHOLESTEROLO + WATER in a rectangular box.
I did energy minimization successfully with following mdp file.
--
;
I have simulations for different peptides in POPC bilayer.
I want to calculate pair distribution function (pdf) between negatively
charged phosphate residue of POPC and positively charged residues of
peptide. Is there any tool available in gromacs for plotting these values?
Secondly, how to
On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote:
I have simulations for different peptides in POPC bilayer.
I want to calculate pair distribution function (pdf) between negatively
charged phosphate residue of POPC and positively charged residues of
peptide. Is there any tool available in
Thank you.
On Sun, Oct 6, 2013 at 8:12 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote:
I have simulations for different peptides in POPC bilayer.
I want to calculate pair distribution function (pdf) between negatively
charged phosphate
Dear Justin
Very thanks for your quick reply.
Depends on how you prepared the system.
For initial structure of system, I used coordination from website:
http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html
Probably there were voids in the solvent or lipid headgroups that caused
On 10/6/13 10:57 AM, shahab shariati wrote:
Dear Justin
Very thanks for your quick reply.
Depends on how you prepared the system.
For initial structure of system, I used coordination from website:
http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html
Note that these lipids require
Commenting out the gmx_fatal() call in src/mdlib/pull.c, line: 331 and
recompiling grompp and mdrun
allows the run to proceed. Everything is stable for 250 ps. I will report if it
fails.
I have posted a redmine at: http://redmine.gromacs.org/issues/1352
Thank you,
Chris.
-- original message
If you want K_on and K_off, then I think you need to look at long-time
equilibrium simulations or massively repeated simulations connected with a MSM.
Beyond that, I believe that you will need to understand all of the important
free energy barriers in all degrees of freedom (hard, to say the
Hi Chris,
I have never done this and I may be missing something. But here is what I
think.
I have seen a few papers use the Arrhenius law, k=A*exp
(-deltaG/kB*T)...-deltaG/kB*T can be obtained from the PMF...Now, if you do
this for different temperatures, you can back out the activation energy and
Dear Rajat:
I just checked the first two papers that you mentioned and they both get
kinetics from standard equilibrium simulations. As for the Arrhenius law, with
k, A, and the energy of activation (Ea) all unknown for each T, how do you
obtain a unique solution for k given T ? Even if you
Dear GROMACS users,
I have been trying to simulate protein of
my interest in lipid bilayer(POPC) . I am following the tutorial of KALP-15
in DPPC. When I try to minimise the system after generating
system_inflated.gro. I get a fatal error from grompp which reads
Hello:
I've submit a simulation in gromacs, and I am just wondering how can
we calculate kinetic constant for the ligand bound/ubound process?
thanks a lot
Albert
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Dear Grzegorz:
From a quick look at your .mdp, I also suggest that you go back to your system
including the peptide that you had managed to finish EM with modified flexible
tip5p but then crashed with the standard rigid tip5p during MD and try the MD
again using gen-vel = yes
if you're still
Dear Sudipta:
on average, bilayers migrate along the positive z axis during gromacs
simulations with a variety of atomistic force fields. This has been reported
before, but never fully resolved ( http://redmine.gromacs.org/issues/165
suggests it is due to rounding ) and I see it all the time.
On 2013-10-04 12:30, Albert wrote:
Hello:
I've submit a simulation in gromacs, and I am just wondering how can
we calculate kinetic constant for the ligand bound/ubound process?
thanks a lot
Albert
Check out our recent paper and references therein:
Hi all
I am running a MD simulation using GPU version of GROMACS 4.6 and I am asked to
use Verlett cut-off scheme.
I am new to GPU computing and I did not find much information about the scheme
in the manual.
I would very thankful if anyone who has used the Verlett scheme can let me know
Dear Users:
I am trying to use the pull code to add a constant force in a particular
direction.
I am getting an error that the initial distance is greater than 1/2 the box
size.
(error in 4.5.5, 4.6.1, 4.6.3)
I must not understand how to use this. I checked the online .mdp options:
Hi,
My name is Insung Na.
I want to introduce certain dihedral's Ryckaert-Bellemans coefficients to
OPLS-AA ffbonded.itp file.
For calculation, I found information on that from Gromacs manual-4.5.6
At equation 4.63, the formula contains F1, F2, F3, and F4.
It seemed that I need those values to
On 10/4/13 10:32 AM, Christopher Neale wrote:
Dear Sudipta:
on average, bilayers migrate along the positive z axis during gromacs
simulations with a variety of atomistic force fields. This has been reported
before, but never fully resolved ( http://redmine.gromacs.org/issues/165
suggests it
Dear gmx-users,
We intend to perform free energy calculations by pulling a polypeptide
along water-hexane interface. We need to pull the polypypeptide from the
water layer towards the hexane layer (crossing the interface). For this we
position restrained one hexane molecule in the bulk of hexane
Sorry forgot to write the subject in previous mail.
Dear gmx-users,
We intend to perform free energy calculations by pulling a polypeptide
along water-hexane interface. We need to pull the polypypeptide from the
water layer towards the hexane layer (crossing the interface). For this we
position
Dear Michael.
The simulations at each lambda point starts from the same structure
that I equilibrated (NPT ensemble) for 20 nanoseconds. The system has
~7500 atoms in a box the size 5 nm x 5 nm x 5 nm. The molecule of
interest is located in the center of the unit cell.
Thanks,
JErnej
Sounds
Hmm. This really isn't quite enough information to go on. Can you
file a redmine issue, and include the files used to generate the run
that crashed (.mdp, .gro,. .top), as well as the files that show it
failing (.log)?
http://redmine.gromacs.org/
On Thu, Oct 3, 2013 at 4:32 AM, Jernej Zidar
Dear Gromacs users,
I have recently written a manuscript titled: Response of the hydrophilic part
of lipid membranes to changing conditions — a critical comparison of
simulations to experiments (http://arxiv.org/abs/1309.2131). To rapidly
improve the manuscript further, we started a public blog
Hi all,
I am trying to compute the order parameters for the sn1 and sn2 chains of
DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3).
I have constructed for each DOPC chain two index files that contains in
the first one all the Carbon atoms where the first Carbon is C=O and the
On 10/3/13 11:50 AM, sa wrote:
Hi all,
I am trying to compute the order parameters for the sn1 and sn2 chains of
DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3).
I have constructed for each DOPC chain two index files that contains in
the first one all the Carbon atoms where
Hi gromacs users,
In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double
bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6
bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to
my C atom. I think, gromacs generate
On 10/3/13 3:08 PM, Ehsan Sadeghi wrote:
Hi gromacs users,
In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double
bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6
bonds). When I do energy minimization in vacuum, I got two F atoms
Thanks Justin. I will try different bond parameters. I usually use PyMol or
Chimera for visualization. Do you have any recommendation for a visualization
software?
Cheers,
Ehsan
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users
On 10/3/13 4:15 PM, Ehsan Sadeghi wrote:
Thanks Justin. I will try different bond parameters. I usually use PyMol or
Chimera for visualization. Do you have any recommendation for a visualization
software?
For quick visualization, VMD (but it often gets bonds wrong if they are not in
line
Dear Gromacs Users/Developers,
I am facing problem for doing umbrella sampling simulation for the
transferring of a small peptide across a membrene in presence of electric
field. Moreover, the simulation was carried out at constant area. Martini
force field for protein, lipid and water was used
Dear users,
I have used grompp command for minimising my system (protein and
membrane). I am getting the error:
---
Program grompp, VERSION 4.5.1
Source code file: confio.c, line: 744
Fatal error:
Invalid line in system.gro for atom 11380:
On 10/2/13 8:21 AM, Andrew Bostick wrote:
Dear users,
I have used grompp command for minimising my system (protein and
membrane). I am getting the error:
---
Program grompp, VERSION 4.5.1
Source code file: confio.c, line: 744
Fatal error:
Dear Justin
Thanks for your quick reply.
What is reason of this issue?
My gro file contains 11383 lines.
11383-3=11380
This value is equal to second line.
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On 10/2/13 8:45 AM, Andrew Bostick wrote:
Dear Justin
Thanks for your quick reply.
What is reason of this issue?
My gro file contains 11383 lines.
11383-3=11380
This value is equal to second line.
Sorry, misread your initial post. One of two things is happening:
1. You've used an
Hi all,
I'm trying to determine the free energy of solvation for a molecule
in n-octanol. I'm separately turning off the Coulomb and Lennard-Jones
interactions as instructed in the free energy tutorial. The
Lennard-Jones simulations keep on crashing for most values of lambda
with the message:
Sounds like the simulation is blowing up. How soon does it start crashing.
Also, what configurations are you using to start your free energy
simulations at each lambda?
On Wed, Oct 2, 2013 at 10:31 PM, Jernej Zidar jernej.zi...@gmail.com wrote:
Hi all,
I'm trying to determine the free
I would generally not try to add it to an existing source repository.
Instead, follow one of the suggestions in
http://www.gromacs.org/Developer_Zone/Git/Gerrit#How_do_I_get_a_copy_of_my_commit_for_which_someone_else_has_uploaded_a_patch.3f
to
check out that version.
Mark
On Tue, Oct 1, 2013 at
Dear Chris,
By now 7ns of the MD passed without a single warning.
Best Regards,
Grzegorz
P.s. The mdp:
constraints = none
integrator = md
dt = 0.001; ps
nsteps = 1000 ; total 10 ns
nstcomm = 1000
nstxout =
Hello everyone,
I would like to calculate angle tetrahedral order parameter of water
molecules as defined by Chau et al (eq 3). I am using g_hydorder of
gromacs 4.6.3 with my index group containing all oxygen atoms of water:
g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out
Hi Mark,
Thank you for your reply. Actually I am not trying to add it to the
repository.
I have gromacs 4.6 installed in my computer. When I was trying using
genbox, an error occurred caused by memory lacking. After searched this
mailing list, I got that extended genbox code that can fix my
On 10/1/13 10:58 AM, Tegar Nurwahyu Wijaya wrote:
Hi Mark,
Thank you for your reply. Actually I am not trying to add it to the
repository.
I have gromacs 4.6 installed in my computer. When I was trying using
genbox, an error occurred caused by memory lacking. After searched this
mailing
Since that patch is already merged, Tegar can just check out the (default)
master branch - see http://www.gromacs.org/Developer_Zone/Git. The CMake
build works the same way. I would suggest just using
your-build-directory/bin/genbox once you have built it, i.e. do not go to
the trouble of
Please provide me with necessary guidance. I have already posted this
thrice but have not got a single reply
Thanks in advance.
On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal nidhikatyal1...@gmail.comwrote:
Hello everyone,
I would like to calculate angle tetrahedral order parameter of water
On 2013-10-01 19:51, Nidhi Katyal wrote:
Please provide me with necessary guidance. I have already posted this
thrice but have not got a single reply
Thanks in advance.
On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal nidhikatyal1...@gmail.comwrote:
Hello everyone,
I would like to calculate
On 10/1/13 1:03 PM, Ehsan Sadeghi wrote:
Hello,
When I use pdb2gmx, the bonds between atoms in the generated conf.gro or conf. pdb file are
misplaced. I am using Avogadro for building the atomistic structure, it uses connect
command to connect atom correctly. After running pdb2gmx, the
Hallo everyone
I would like to know if anyone has installed gromacs4.6.3 with CPMD, or how
to monitor this installation?
I couldn't find the installation procedure in the manual of gromacs4.6
I am looking forwards any suggestions.
Thanks
Collins
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gmx-users mailing list
Greetings
I have a large protein of 303 residues and one of the lysine is acetylated
in the same.
The forcefield selection according to the options says as follows:
Residue 'ALY' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
On 9/30/13 5:19 AM, suhani nagpal wrote:
Greetings
I have a large protein of 303 residues and one of the lysine is acetylated
in the same.
The forcefield selection according to the options says as follows:
Residue 'ALY' not found in residue topology database
For more information and tips
Thanks Justin,
I modified the pdb file, but it cannot recognize my residue LIG. Here is the
error:
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading nafion5.pdb...
Read 46 atoms
Analyzing pdb file
Splitting chemical chains based on TER records
On 9/30/13 12:50 PM, Ehsan Sadeghi wrote:
Thanks Justin,
I modified the pdb file, but it cannot recognize my residue LIG. Here is the
error:
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading nafion5.pdb...
Read 46 atoms
Analyzing pdb file
Yes, I have introduced the new .rtp entry in
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp.
What could be wrong?
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Monday, September 30, 2013
On 9/30/13 2:23 PM, Ehsan Sadeghi wrote:
Yes, I have introduced the new .rtp entry in
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp.
What could be wrong?
The outcome defies logic. If the .rtp entry were in that file, pdb2gmx would
not throw that error. Can you
One a system passes EM and a couple of ps of MD, is it always stable
indefinitely? If not, then
something is wrong somewhere.
-- original message --
Dear Chris,
I put one tip5p molecule in a center of dodecahedral box - 2nm from that
molecule to walls, filled it with tip5p, ran 6000 steps of
On 9/30/13 4:40 PM, Ehsan Sadeghi wrote:
Many thanks Justin.
Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx
works and I can start the modelling.
In the future, make sure you're providing accurate answers to the questions
being asked. I asked about this
I was pretty confident that I am modifying the right file. apparently I did not
access to the main file; so I asked my supervisor and he provided me with a
proper access to the files.
Thanks again Justin.
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for
Many thanks Justin.
Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx
works and I can start the modelling.
I also have some concern about my pdb file. i generated from my drawing in
Avogadro, with some arbitrary bond length and angle. I hope that I can find
the
Dear all,
I want to install Extended Genbox from gerrit.
https://gerrit.gromacs.org/#/c/1175/
How can I put this code into my existing gromacs installation?
Thanks.
Regards,
Tegar
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Dear all,
I have a basic doubt regrading g_membed.
Is it compulsory to solvate the membrane system before the protein's
insertion or can we solvate after the protein's insertion?
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of
Dear Chris,
Authors answered me very quickly. They did not have such a problem, but
I still don't know the details of their input. They used gromacs-3.3, so
I decided to give the old one a try. I did some tests with 3.3.4.
Although the same problem occurred during steep minimization, some
Dear Grzegorz:
Under no conditions should any of the tip5p geometry change (for the standard
tip5p model).
If you find that this is happening, then that is certainly an error. You can
check if you like by analyzing
your trajectory. However, flexible bonds will allow the distance from the
Dear gromacs users,
I just realized that even after trying to re-start a run, i still got separate
name files (idk why), but I managed to combine err, xtc files, but don't know
how to bring 2 .cpt files together, or is it not required? I'm trying to do NPT
run next, and it will -t *.cpt, but I
On 9/28/13 9:41 PM, Abu Naser wrote:
Hi all users,
Is it possible to add hydrogens to some of the selected atoms in the system
using pdb2gmx?
pdb2gmx is a rather complex way to do it. g_protonate is the tool for adding
hydrogens to a configuration, but note it can only handle PDB files
On 9/29/13 1:24 AM, Jonathan Saboury wrote:
I want to run a simulation of cyclohexane in deuterated chloroform.
I was able to run a sim of cyclohexane in regular chloroform, but unable to
find how to make a solvent deuterated. I know that pdb2gmx has a -heavyh
and -deuterate option, would I
On 9/29/13 2:32 PM, Xu Dong Huang wrote:
Dear gromacs users,
I just realized that even after trying to re-start a run, i still got separate
name files (idk why), but I managed to combine err, xtc files, but don't know
how to bring 2 .cpt files together, or is it not required? I'm trying to
Dear Chris,
I did not post the redmine issue yet, I want to check every possibility
beforehand. I will analyze trajectories more closely now.
Best,
Grzegorz
On 2013-09-29 18:47, Christopher Neale wrote:
Dear Grzegorz:
Under no conditions should any of the tip5p geometry change (for the
Dear Chris,
I put one tip5p molecule in a center of dodecahedral box - 2nm from that
molecule to walls, filled it with tip5p, ran 6000 steps of steep
minimization. After another 2704 steps of cg it converged to emtol 1.0.
I run 100k steps of nvt on this box afterwards
Dear all users
I would like to calculate pc loadings for various integrated factors in the
form of following sample table:
Integrated Factors
PC1
PC2
PC3
PC4
PC5
PC6
PC7
PC8
PC9
PC10
Total non polar surface area
0.60
-0.07
-0.76
-0.11
0.08
0.05
-0.16
0.08
-0.01
0.02
Native
Hi Prathiba,
I think you should have a look at the Functional Mode Analysis method
from Bert de Groot's lab.
Cheers,
Tsjerk
On Sat, Sep 28, 2013 at 8:13 AM, pratibha kapoor
kapoorpratib...@gmail.comwrote:
Dear all users
I would like to calculate pc loadings for various integrated factors
Hello:
I am trying to analyze the water density along Z direction of my protein.
Here is my g_select command:
g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf
select.dat
and here is my select.dat:
waterO = water and name OW and z30 and z70;
close = water0 and within 0.4
Hi,
I am not sure, but try resname SOL or something similar. Also, your first
line has waterO and second line has water0.
On Sat, Sep 28, 2013 at 1:00 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I am trying to analyze the water density along Z direction of my protein.
Here is my g_select
On 09/28/2013 09:42 AM, rajat desikan wrote:
Hi,
I am not sure, but try resname SOL or something similar. Also, your first
line has waterO and second line has water0.
Hi Rajat:
thanks a lot for such kind and helpful comments. It works now. I run it
by command:
g_select_mpi -f
Hi all,
I want to put off constraint between some bonds in my system based on their
atom numbers but the .gro file and .top file atom numbers do not match,
because I used .pdb file to generate this .top file using pdb2gmx. (the top
files contains the atom numbers based on this initial input .pdb
Dear Gigo:
everything that I suggested was just ways that you might get a system without
bad contacts to
start your simulation with the proper (standard) tip5p model and oplsaa. I
expected that combination
to work together since they came out of the same lab, but looking at the
initial tip5p
On 9/28/13 11:20 AM, bipin singh wrote:
Hi all,
I want to put off constraint between some bonds in my system based on their
atom numbers but the .gro file and .top file atom numbers do not match,
because I used .pdb file to generate this .top file using pdb2gmx. (the top
files contains the
Hello gromacs users,
I restarted my run due to power failure using mdrun -v -s .tpr -cpi
.cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make
it so it continues to update the original .xtc and .tpr files?
Thanks,
Xu Huang
Research Assistant
Chemical
On 9/28/13 2:46 PM, Xu Dong Huang wrote:
Hello gromacs users,
I restarted my run due to power failure using mdrun -v -s .tpr -cpi
.cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make
it so it continues to update the original .xtc and .tpr files?
If you're
Justin,
I see. Is there a way to *stitch* the two files together so I can continue onto
a NPT run?
On Sep 28, 2013, at 2:49 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/28/13 2:46 PM, Xu Dong Huang wrote:
Hello gromacs users,
I restarted my run due to power failure using mdrun -v -s
On 9/28/13 2:52 PM, Xu Dong Huang wrote:
Justin,
I see. Is there a way to *stitch* the two files together so I can continue onto
a NPT run?
Appending is the default behavior of mdrun, if invoked properly and the files
haven't been messed with. If not, trjcat appends trajectories and
I see,
Thank you for the information Justin.
On Sep 28, 2013, at 2:57 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/28/13 2:52 PM, Xu Dong Huang wrote:
Justin,
I see. Is there a way to *stitch* the two files together so I can continue
onto a NPT run?
Appending is the default
Dear Chris,
I am really grateful for your help. This is what I did, with additional
LJ terms on LP1 and LP2 of tip5p:
- 5000 steps of steepest descent with positions restraints on protein
and flexible water (flexibility like in tip4p),
- 5000 steps of steep, no restraints, flexible water,
-
Hi all users,
Is it possible to add hydrogens to some of the selected atoms in the system
using pdb2gmx?
With best regards,
Naser
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* Please
Dear Gigo:
that's a good comprehensive testing and report. Please let us know what you
find out from those authors.
Their paper was short on methods (unless I missed it... I didn't check for any
SI), so perhaps they did something
non-standard and didn't report it.
I think at this point it is a
I want to run a simulation of cyclohexane in deuterated chloroform.
I was able to run a sim of cyclohexane in regular chloroform, but unable to
find how to make a solvent deuterated. I know that pdb2gmx has a -heavyh
and -deuterate option, would I do it this way? It isn't a protein and would
Yes.
Cheers,
Tsjerk
On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy venkat...@gmail.com wrote:
Thanks for the quick reply sir.
So, does it mean I can apply trjcat on the processed xtc files???
On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi Venkat,
Thank you sir.
On Fri, Sep 27, 2013 at 11:47 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Yes.
Cheers,
Tsjerk
On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy venkat...@gmail.com wrote:
Thanks for the quick reply sir.
So, does it mean I can apply trjcat on the processed xtc files???
Dear all gmx users
I would like to calculate pc loadings for various integrated factors in the
form of following sample table:
Integrated factorsPC1PC2PC3 PC4PC5PC6PC7PC8 PC9PC10Total nonpolar surface
area0.60 -0.07-0.76-0.11-0.060.11 0.05-0.160.06-0.02Chain exposed area 0.92
-0.14-0.050.12
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