to do with single or double precision?
On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Are those variables actually showing up in your environment?
On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic
mariagorano...@gmail.comwrote:
Dear All
I am trying
...@gmail.comwrote:
Yes, I can see them in printenv
does this have anything to do with single or double precision?
On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Are those variables actully showing up in your environment?
On Thu, Dec 27, 2012 at 11:31 AM, maria
PM, maria goranovic
mariagorano...@gmail.comwrote:
I will try to fix this. Thank you.
Now, the problem I have is that the executables all belong to root, and as
a user, I am unable to execute them. How to fix this little one?
Maria
On Thu, Dec 27, 2012 at 3:36 PM, Mark Abraham mark.j.abra
Unfortunately, g_dih was written before 1997 and its documentation is very
poor. It does not actually read the connectivity in the .tpr file, nor does
it attempt to infer connectivity other than for some protein backbone
dihedrals. For some reason, it thinks it finds some for your topology, but
On Thu, Dec 27, 2012 at 12:32 AM, Gert Peters gert.pet...@ugent.be wrote:
Hi everybody,
Im trying to use GROMACS for MD of a RNA model generated by Rosetta
(FARFAR). As a test I try processing a modelledpdb file. When I prepare
thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh
) from
Unfortunately, it means what it says. Xcode by default does not install the
command line compilers, so you might need to Google the solution for that.
Mark
On Tue, Dec 25, 2012 at 1:03 PM, maria goranovic
mariagorano...@gmail.comwrote:
Dear All
I have a macbook pro, with mountain lion, with
mdrun -rerun your-old-trajectory
works. Unfortunately you're asking us to guess what you did wrong, without
giving us any detail of what you did... that's tricky :-)
Mark
On Tue, Dec 25, 2012 at 12:09 AM, xiaowu759 xiaowu...@gmail.com wrote:
Dear Justin,
I am sorry to spell the word. In
Check out http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
On Mon, Dec 24, 2012 at 5:35 PM, Ankita naithani
ankitanaith...@gmail.comwrote:
Hi,
I am running a protein simulation for 70 ns. I had a MPI run but due
to my time constraints on the server, it stopped after 28ns. Now, I
g_analyze -h probably has relevant things to say
On Mon, Dec 24, 2012 at 10:56 PM, zifeng li lizife...@gmail.com wrote:
Hi, Gromacs users,
I'm using Gromacs 4.5.4 and wondering how is the Err.Est given by
g_energy calculated? Is it roughly
standard deviation/ sqrt N
N is the independent
On Wed, Dec 19, 2012 at 11:27 PM, Ahmet yıldırım ahmedo...@gmail.comwrote:
Dear users,
When analyzing some of the simulations;
I get 312 K, 310 K or 308 K instead of 300K (the t_ref value for the whole
system).
1. What is the reason for the increase of temperature? For example it can
be
On Mon, Dec 17, 2012 at 6:01 PM, Albert mailmd2...@gmail.com wrote:
hello:
I reduced the GPU to two, and it said:
Back Off! I just backed up nvt.log to ./#nvt.log.1#
Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precision)
This is a development version from October 1.
crash point without error.
best,
dawei
On Thu, Dec 13, 2012 at 12:17 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
1) AFAIK there are indeed conditions under which domain decomposition
does
not work with distance restraints
2) Your symptoms could just be that (some
On Fri, Dec 14, 2012 at 3:46 PM, Thomas Schlesier schl...@uni-mainz.dewrote:
Dear all,
i have a small question regarding the '-nosum' option of 'mdrun'.
The manual states:
For a global thermostat and/or barostat the temperature and/or pressure
will also only be updated every nstlist steps.
That looks very strange. Please file an issue at
redmine.gromacs.orgincluding all your .tpr and .cpt, and assign it to
me.
Mark
On Thu, Dec 13, 2012 at 1:07 PM, Kenny Bravo Rodriguez
ke...@mpi-muelheim.mpg.de wrote:
Hi all,
and thanks Mark, Chris and Xavier for your comments.
I finally
1) AFAIK there are indeed conditions under which domain decomposition does
not work with distance restraints
2) Your symptoms could just be that (some of) your initial conditions, or
them in combination with the restraints are problematic. Without more
description about why and how you're using
That shouldn't happen - looks like a memory problem. There's no value to
you here in running in double precision - does the problem occur with
single-precision trjconv?
Mark
On Thu, Dec 13, 2012 at 4:47 PM, Wall, Michael E mew...@lanl.gov wrote:
possible bug in trjconv -split.
I'm using the
You can just turn the power off :-) The checkpointing mechanism ensures you
already have all your output up to the time of the last checkpoint (default
every 15 minutes). You can use gmxcheck on these files during the
simulation to see what's in them.
Mark
On Wed, Dec 12, 2012 at 10:26 AM, Ali
On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I was calculating solvent accessible surface area for a trajectory
using g_sas. I used an index file with 3 sets (A, B, C) of mutually
exclusive residues but summing up to 20 amino acids. Then using
g_sas
Unix signals SIGTERM and SIGUSR1 can be sent to mdrun that will cause it to
stop next step or next neighbour search step. That ensures an orderly
termination, inasmuch as the file system buffering then has time to flush
before the power goes off :-) Various shell or queue system commands can
send
We specialise in building trees, unfortunately :)
On Wed, Dec 12, 2012 at 9:04 PM, Keith kh...@khuws.plus.com wrote:
Thanks, couldn't see the wood for the trees. Clear as daylight now.
On 11/12/12 19:39, Mark Abraham wrote:
Yes. Read about analysis groups in chapter 8.
Mark
On Tue
Section 7.4 and chapter 8 of the manual discuss what functionality exists
in the utility tools. If that doesn't help you need to be more specific
about what you mean by calculate interactions
Mark
On Tue, Dec 11, 2012 at 2:15 PM, Wu Chaofu xiaowu...@gmail.com wrote:
Dear gmxers,
I am trying
No. Bonded interactions (such as distance restraints) can only be defined
between atoms present in the same [moleculetype]. OTOH a [moleculetype]
doesn't care whether any bonded interactions exist between its atoms or
not, so as long as you obey the constraint that the atom ordering implied
by
1. Run mdrun with nstfout set appropriately
2. g_traj -h
3. g_analyze -h
4. Profit!
Mark
On Tue, Dec 11, 2012 at 3:31 PM, khuws kh...@khuws.plus.com wrote:
Hi
Does anyone know if, and if so how, GROMACS can generate a force
autocorrelation function?
If this is not possible then can I
We don't yet have enough information to help you. What GROMACS version?
Does it happen under other conditions?
Mark
On Tue, Dec 11, 2012 at 9:06 AM, vahid garshasbi v.garsha...@gmail.comwrote:
hi
when I run g_density in X AND Y direction in my program I have this error:
*** glibc detected
Yes. Read about analysis groups in chapter 8.
Mark
On Tue, Dec 11, 2012 at 8:20 PM, khuws kh...@khuws.plus.com wrote:
Thanks,
I forgot to mention that I need the force autocorrelation for the forces
acting on a single atom. Will the method
1. Run mdrun with nstfout set appropriately
2.
Hard to say. Your compiler is prehistoric, and things to do with pthreads
are the province of the compiler, so getting a more recent version will
probably fix it.
Mark
On Mon, Dec 10, 2012 at 7:32 AM, BHARATI DUTTA bharati.du...@piramal.comwrote:
Hi,
The following error pops up during
Correct, C1060 does not have the CUDA 2.0 compute capability required for
GROMACS 4.6. We will not have the ability to support GPU cards of lower
capability in the future. Unfortunately, your only GROMACS options are
probably to use the OpenMM functionality in 4.5.x (which is still present
in 4.6,
Indeed, thanks Javier.
These kinds of features are a bit awkward to document because there are
lots of conditions under which various forms of interaction generation are
used - primarily varying with the forcefield. Different force fields
motivate various capabilities of pdb2gmx and it's not
, Dec 10, 2012 at 11:51 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
Indeed, thanks Javier.
These kinds of features are a bit awkward to document because there are
lots of conditions under which various forms of interaction generation are
used - primarily varying with the forcefield. Different
On Mon, Dec 10, 2012 at 9:48 PM, francesco oteri
francesco.ot...@gmail.comwrote:
Dear gromacs users,
I am facing a very tricky problem in building a stable topology.
In particular I am trying to use MARTINI force-field and I noticed that if
I use a box whose the side size is smaller than
On Mon, Dec 10, 2012 at 11:15 PM, francesco oteri francesco.ot...@gmail.com
wrote:
Actually, since I copied and pasted the mail, there is an imprecision. When
I use 20nm as box side lenght I don't get
any error, everything goes fine.
I actually tested different size between 19 and 20 nm and
On Mon, Dec 10, 2012 at 11:44 PM, francesco oteri francesco.ot...@gmail.com
wrote:
Hi Mark,
you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
use 0.21. Since I still got errors with this procedure, I decided to remove
water manually through vmd.
Don't change things
On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/10/12 5:45 PM, francesco oteri wrote:
For Justin,
I need this water for one simple reason: less then 20nm doesn't workAs
I said before
It seems you have identified the source of the problem, and it is
Yukun Wang
PhD candidate
Institute of Natural Sciences College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai
2012/12/7 Mark Abraham mark.j.abra...@gmail.com
Hi all,
We've updated the GROMACS beta version to fix some
Hi Yukun,
In future, please only target email associated with GROMACS development to
the gmx-developers mailing list. gmx-users is for usage questions, such as
installation issues. I am replying to this email to both lists.
If you've correctly installed and used icc 11.1, then I think you should
See
http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite
On Fri, Dec 7, 2012 at 9:08 AM, BHARATI DUTTA bharati.du...@piramal.comwrote:
Hi Justin,
I am trying to install gromacs-4.5.5 on a Linux work station (x86_64) but
I am getting
What components will that potential energy have?
Mark
On Mon, Dec 3, 2012 at 6:54 PM, James Starlight jmsstarli...@gmail.comwrote:
Dear Gromacs Users!
I'm simulating different complexes of the receptors with different ligands.
For each complex I want to determine potential energy (not the
2fs is normally considered too large a time step for stable integration
with only bonds to hydrogen constrained, so your observation of
non-reproducible LINCS warnings is not indicative of some other problem.
Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK this
works fine,
On Tue, Dec 4, 2012 at 5:30 PM, sebastian
sebastian.wa...@physik.uni-freiburg.de wrote:
On 12/04/2012 05:09 PM, Mark Abraham wrote:
2fs is normally considered too large a time step for stable integration
with only bonds to hydrogen constrained, so your observation of
non-reproducible LINCS
Looks like a compiler bug to me, and google agrees
http://gcc.gnu.org/bugzilla/show_bug.cgi?id=47318.
Even if there were not this bug, we would strongly encourage you to get the
better performance available from more recent versions of gcc. I was about
to suggest 4.6 or newer, but the above URL
Not easily - a complex geometric criterion is needed to define a
multi-molecule H-bonding bridge.
g_hbond can probably be made to do the simple case with 1 bridging water,
but anything more complex than that will need the functionality of g_select.
Mark
On Fri, Nov 30, 2012 at 10:31 AM, Albert
On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul jalem...@vt.edu wrote:
Hooray for being the first to report a problem with the beta :)
:) Thanks!
We have a cluster at our university that provides us with access to some
CPU-only nodes and some CPU-GPU nodes. I'm having problems with
On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/30/12 8:21 AM, escajarro wrote:
I do have constraints, all the bond lengths are fixed and they are
specified
in the topology file. Am I doing something wrong? I copy here the
definition
of one of the models I
Thanks. http://redmine.gromacs.org/issues/1053 created.
Mark
On Fri, Nov 30, 2012 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/30/12 11:00 AM, Mark Abraham wrote:
On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/30/12 8:21 AM, escajarro wrote:
I
You need to name libraries with FFTW3F_LIBRARIES, not the library path.
That explains the dropped dependency and subsequent problems.
Mark
On Mon, Nov 26, 2012 at 4:19 PM, Stefan Jasconek
stjas...@students.uni-mainz.de wrote:
Dear Users,
I have problems with the installation of GROMACS 4.5.5
Look at the top of the output of any GROMACS program.
Mark
On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
Is any gromacs command which can tell us or distinguish whether what
installed is gromacs 4.5.4 or 4.5.5?
Cheers,
Acoot
--- On Sat, 24/11/12,
Check out the Bjelkmar paper that introduced CHARMM27 into GROMACS, cited
from the manual section about CHARMM (hint, hint)
Mark
On Sat, Nov 24, 2012 at 5:36 PM, Albert mailmd2...@gmail.com wrote:
hello:
I found that some people use CHARMM27+t3p for their simulation system,
and some
Hi,
The GPU functionality available in GROMACS 4.5 based on OpenMM is likely to
be deprecated because we lack the resources to continue to support it - as
you can see from the limited documentation you can see for it on our
website. I would advise against attempting to build or use anything other
the (let be it converged) simulation from
different starting conditions in order to add that valuable statistics
you
mention?
I think this was Albert's question
Felipe
On 11/21/2012 12:41 PM, Mark Abraham wrote:
If a simulation ensemble doesn't converge reliably over a given time
scale
If a simulation ensemble doesn't converge reliably over a given time scale,
then it's not converged over that time scale. Repeating it from different
starting conditions still adds valuable statistics, but can't be a
replicate. Independent replicated observations of the same phenomenon allow
you
) simulation from
different starting conditions in order to add that valuable statistics you
mention?
I think this was Albert's question
Felipe
On 11/21/2012 12:41 PM, Mark Abraham wrote:
If a simulation ensemble doesn't converge reliably over a given time
scale,
then it's not converged over
Virtual sites also have a hidden benefit - not only can you take a longer
time step, but the width of the distribution of PE is relatively wider, so
you can have higher exchange probability for the same temperatures.
Mark
On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale
And get the use of radians right!
Mark
On Nov 15, 2012 4:01 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi,
15 nov 2012 kl. 15.41 skrev Laura Leay:
Thanks Eric,
Just to clarify (I hope this notation is in fact clear):
E=0.5k [ 1 - cos( n*phi - n*phi_o +180 ) ] = 0.5k [ 1 +
You'll have to find the authors of it and read what they wrote about it.
Mark
On Wed, Nov 14, 2012 at 7:38 PM, Albert mailmd2...@gmail.com wrote:
hello:
I found that there is a CHARMM22star FF in Gromacs website, it is said
was developed by Deshaw group instead of the one in Maryland. I am
On Fri, Nov 9, 2012 at 3:29 PM, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
Dear Dejun:
I don't know why --enable-bluegene gives you problems or what it is
supposed to do. Was the BGQ even
available when gromacs 4.5.5 came out? I doubt it.
There's no code currently optimized for
mdrun will not leak memory that badly. I would guess your output buffers
are not being flushed, so grow without bound.
Mark
On Oct 25, 2012 12:36 AM, Pablo Serra se...@famaf.unc.edu.ar wrote:
Dear users,
I'm running a NVT simulation with gromacs 4.5.5,using
the command:
Yes. Back up your files, try it and see. ;-) Note that REMD is no more
time consuming than each component simulation. More resources are
consumed, however.
Mark
On Oct 21, 2012 9:15 PM, Albert mailmd2...@gmail.com wrote:
hello:
I found that the REMD is really time comsuing MD and it will over
On 12/10/2012 6:27 PM, Jianguo Li wrote:
One situation is the analysis that require velocities, such as calculating
velocity autocorrelation function or lateral pressure.
Or forces, for some reason. Also see
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
On 5/10/2012 3:55 PM, mohammad agha wrote:
Dear Justin,
Thank you very much.
So, decreasing of box dimensions is not bad, if all thing process natural, yes?
The cause of my doubt was because of in the most of articles was said for example
we select box with dimensions 10nm that after
Message -
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, October 5, 2012 9:34 AM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 3:55 PM, mohammad agha wrote:
Dear Justin,
Thank you very much.
So
On 4/10/2012 5:10 PM, Albert wrote:
hello:
I found that the .trr from mdrun output is really much huger than
the .xtc file. However, most people would like to generate the .trr
file and then convert it into .xtc file.
See
On 5/10/2012 12:06 AM, mohammad agha wrote:
Dear GROMACS Users,
I asked this question before but I don't understand it!
I placed several materials in my box of simulation for example box with
6nm*6nm*6nm and my materials are not placed in the smaller box but when I
equilibrate my system,
On 5/10/2012 1:49 AM, lloyd riggs wrote:
Please choose descriptive subjects and start new email messages when
posting to mailing lists. This makes people better able to respond to
you by allowing mail reading software to work properly. Cross-posting to
the VMD and GROMACS lists when your
On 4/10/2012 3:37 PM, Deepak Ojha wrote:
Dear All
I want to use Amber force field in Gromacs therefore I installed the
latest version of Gromacs and
installed accordingly as per as the instructions given in INSTALL.automake file.
./configure
make
make install
It works fine and shows the message
On 24/09/2012 4:49 PM, Andreas Zink wrote:
Dear all,
I've done some REMD simulations using a quite high exchange attempt
frequency (10 attempts per ps) as proposed by Sindhikara et al.
(Exchange Often and Properly in Replica Exchange Molecular
Dynamics,J. Chem. Theory Comput. 2010, 6,
On 21/09/2012 11:08 PM, Bastien Loubet wrote:
Justin Lemkul wrote
On 9/21/12 8:29 AM, Bastien Loubet wrote:
Dear gmx users,
We recently got a problem with the rerun feature of mdrun, and we request
your help in order to help to solve it.
We have run a simulation of a large POPC membrane
On 23/09/2012 5:22 PM, mohan maruthi sena wrote:
Hi all,
I want to do normal mode analysis for a protein using elastic
network model containing 691 residues. I consider only c-alpha atoms
connected by a spring constant of 81600 kj/nm2. When I do normal mode
analysis I get the
On 20/09/2012 1:08 PM, Rajiv Gandhi wrote:
Dear all,
Why all people cut the protein ligand bond to produce the photodissociation?
Because MM forcefields typically assume bonds do not break or form.
Electronic degrees of freedom are not directly considered in the model.
For instances, In
the distance between atom no. 500 (protein
backbone) and atom no. 879 (ligand atom) with respect to time)
See manual 8.1 for discussion, and
http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx for more.
Mark
On Thu, Sep 20, 2012 at 10:20 AM, Mark Abraham mark.abra...@anu.edu.au wrote
On 20/09/2012 4:34 PM, Ladasky wrote:
Justin Lemkul wrote
So the initial equilibration was NPT?
Yes.
Justin Lemkul wrote
Did you ever try simply running NVT with
either Berendsen or V-rescale before applying any type of pressure
coupling?
No, I haven't, and I don't remember seeing that
On 20/09/2012 5:08 PM, Ladasky wrote:
Mark Abraham wrote
This all sounds much like an issue with the topology or starting
configuration.
And it is for that reason that, during my debugging process, I switched back
from the chimeric protein structures that I was building myself to a
standard
On 20/09/2012 7:31 PM, tarak karmakar wrote:
Dear All,
I need to plot a specific dihedral in my protein and I have to
see how it is changing with time. So while doing that I have created a
new group for that specific dihedral by taking corresponding 4 atoms.
Now, how could I specify
On 20/09/2012 7:26 PM, Wu Chaofu wrote:
Dear gmxers,
I have generated MD simulation trajectory using gmx, and now I want to
recalculate the energies and forces for the older trajectory by
excluding interactions between two defined groups. Therefore, the
older trajectory is used as one input
On 20/09/2012 9:35 AM, Peter C. Lai wrote:
I am not sure where the idea of using berendsen barostat with the v-rescale
thermostat for equilibration came from, however. Doesn't the typical
equilibration begin with v-rescale for temperature equilibration then
adding parinello-rahman barostat then
On 21/09/2012 11:35 AM, Rajiv Gandhi wrote:
Dear all gromacs users,
In myoglobin system, how we can cut the bond between Fe-C to produce the
photodissociation through MD?.
By not making it in your topology. Whatever procedure you follow for
making the other Fe-C interactions needs to differ
On 19/09/2012 4:37 PM, Tsjerk Wassenaar wrote:
g_bond.c / gmx_bond.c ?
No, I checked earlier and it uses index groups. trjconv -pbc whole is no
good either.
Mark
Cheers,
Tsjerk
On Sep 18, 2012 9:50 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 19/09/2012 12:49 PM, Amit Shavit
On 19/09/2012 11:22 PM, Ali Alizadeh wrote:
Dear Justin
I prepare a .top file with a combination of input #include and pdb2gmx,
How can i generate a .gro file from this .top file?
You can't - they have radically different kinds of information. Also,
see
On 20/09/2012 7:10 AM, Ladasky wrote:
After weeks of trying various conditions, I found my problem. Here, from my
position-restrained MDP file, are the two relevant lines:
; Temperature coupling is on
tcoupl= V-rescale ; Weak coupling for initial equilibration
[snip]
; Pressure
On 20/09/2012 2:05 PM, tarak karmakar wrote:
Thanks Justin.
But in my case I want to plot the distance between one atom in the
backbone of the protein and other atom present in the ligand. Then how
can I specify these two atoms I need for plotting the distance between
them.
g_dist treats the
On 18/09/2012 11:21 PM, Bharath K. Srikanth wrote:
Hi all
While attempting to simulate the self assembly of a course-grained DSPC
lipids, I ran into a problem using the genbox command.
I first used genbox to create a box of 32 DSPC lipids, of dimensions 20 x
20 x 20 nm^3. The command used was
On 19/09/2012 12:49 PM, Amit Shavit wrote:
Hello,
I'm relatively new to GROMACS, and I need to write some of my own analysis
tools using the template.c file.
I have been able to figure out most of the structure of it, and how the C
Structs are used. That is to say, I can successfully retrieve
On 17/09/2012 11:50 AM, vidhya sankar wrote:
Dear Mark,
Thank you for your reply
I have used the peptide FLF
For that pdb2gmx construct topology successfully with -ter choosing any thing
for both terminal.
OK, well you can work with that topology as your
On 17/09/2012 10:01 PM, tarak karmakar wrote:
Dear All,
I want to have one of tyrosine residues in my protein to
be unprotonated. I am using amber force field for the simulation. But
in aminoacid.rtp there is no entry for the unprotonated one. So I am
adding it by myself in to the
On 16/09/2012 11:49 PM, Ankita naithani wrote:
Hi,
I am trying to use g_confrms to compare my initial and final structure
and fit them on their backbone. However, I notice a difference of 10
atoms in both of these structures and so I am unable to use g_confrms.
Can anyone please help me and
. Could you please suggest the possible
reason for the difference?
Somewhere between initial and final you changed the composition.
Only you know what what those states were and what you did between them :-)
Mark
On Sun, Sep 16, 2012 at 3:03 PM, Mark Abraham mark.abra...@anu.edu.au wrote
On 17/09/2012 2:55 AM, vidhya sankar wrote:
Dear Mark ,
AgainThanks for you reply
After Editing my pdb file from intial FL to FLF format
Then i Run pdb2gmx for my linaerpdb file , i have selected none for both
termini ( with -ter option) as you mailed
On 15/09/2012 9:12 PM, Shima Arasteh wrote:
Hi all,
Does anybody know where can I get the lipid.itp file defined by CHARMM ?
I have the popc.itp and popc.pdb files generated by CHARMM36. But what about
the lipid.itp file?
Google knows ;-)
Mark
--
gmx-users mailing list
On 16/09/2012 12:17 AM, James Starlight wrote:
In that case I've obtain error
Fatal error:
Failed to lock: md_init.log. Already running simulation?
What does it means ? the md_init.log is present in the wor dir
Appending to an old run requires that all the filenames are identical
between
On 12/09/2012 11:29 PM, Mohsen Ramezanpour wrote:
Dear All
Actually I am very interested to know the list of works which have
used Gromacs for their work.
I searched in both google scholar and scopus, but the results are not the same!
of course I looked for all articles that have cited
On 13/09/2012 2:42 AM, Rajiv wrote:
Dear all,
I would like to measure the rotation angle of helix movement during MD
simulation course. Can you tell me how can I measure and make that rotation
angle plot ? Thanks.
Have a look in manual sections 7.4, chapter 8 and then Appendix D. You
can
On 13/09/2012 4:33 PM, Bharath K. Srikanth wrote:
Hi
I am trying to simulate the self-assembly of course-grained DSPC lipids
into a lipid bilayer. I made a box (7.5 x 7.5 x 7.5) containing 128 DSPC
lipids, and added 768 molecules of water to the system, and ran a
minimization (using em.mdp).
On 15/09/2012 1:37 PM, vidhya sankar wrote:
Dear Justin and other Gromacs users ,
Thank you for your previous reply
Again i Have tried the option -missing when i use pdb2gmx tool i
have got errror as follows
My command is
./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro
On 15/09/2012 3:16 PM, Shima Arasteh wrote:
Dear users,
I rotated my protein to set in a proper direction:
# editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro
The generated protein-rotate.gro is something unusual, because the residue
numbers and residue names are ordered
On 15/09/2012 3:33 PM, Shima Arasteh wrote:
I need to say that I generated .pdb file of protein-rotate.gro .Yes, the
lines sent you, are from the pdb file.
You can't get effective help if you won't describe your method
precisely. First, you claimed the generated .gro was unusual by
On 11/09/2012 2:36 AM, James Starlight wrote:
Dear Gromacs Users!
I'm simulating intrinsic dynamics of some membrane receptors which can
have functional relevance. Therefore I'm looking for the most suitable
initial conditions of my simulation which could provide maximal degree
of such
On 11/09/2012 7:55 AM, Andrew DeYoung wrote:
Hi,
In the [ atoms ] section of an .itp file, there is a column (cgnr) where a
charge group number is given (an integer). This cgnr column is shown in,
for example, the manual version 4.5.4 in Section 5.7.
My question is, do the charge group
On 11/09/2012 2:04 PM, xiaojing gong wrote:
Dear all,
When use the V-rescale algorithm , how to choose the time
constant value, I saw some choose 0, some choose 0.1 ps.
Are there some standard for choosing the time constant?
The effects of these choices are discussed in
On 11/09/2012 2:02 PM, xiaojing gong wrote:
Dear all,
Typically, we use over 100 ns to simulate the transport progress.
But *How the sufficient number of iterations and these times has been
determined? Are there some convergence tests ?*
There ought to be, but in practice things vary
On 11/09/2012 1:33 PM, Nur Syafiqah Abdul Ghani wrote:
Dear all users,
I had this problem and i dont know how to solve it.I need to create
other co-solvent which does not have in pdb bank.
I to optimize it by using GAMESS software and do RESP for charge
calculation.When i do all this part there
On 9/09/2012 11:41 PM, ramesh cheerla wrote:
Dear Gromacs users,
Recently I have converted each frame of the
trajectory to a pdb file using gromacs tool g_trjconv and then
have extracted angles from the CRYST1 record of pdb file, to see how
they are varying in
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