Thank you!! But it still didn't work!!
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I changed the cut-offs as follows, still isn't helping. I tried restraining
the urea which also didn't work. I have attached the topology as well.
topolurea.top
http://gromacs.5086.x6.nabble.com/file/n5009723/topolurea.top
*The nvt.mdp*
title = UREA_in_WATER NVT equillibration
;define
Hi,
Is affinity setting (pinning) on? What compiler are you using? There
are some known issues with Intel OpenMP getting in the way of the
internal affinity setting. To verify whether this is causing a
problem, try turning of pinning (-pin off).
Cheers,
--
Szilárd
On Tue, Jul 9, 2013 at 5:29
constraints
freeze_grps
virtual_sites
Cheers,
Tsjerk
On Jul 9, 2013 10:36 PM, Nash, Anthony anthony.n...@warwick.ac.uk wrote:
Hi all,
I would imagine this has been covered before, yet I don't think I have
unearthed the right search inquiry yet.
I want to make a dihedral angle along the
Hey :)
You can use editconf -scale to scale the system to the average box size.
Cheers,
Tsjerk
On Jul 9, 2013 4:28 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de
wrote:
On 09.07.2013 16:11, Neha wrote: I had a question about trjconv. After
one of my simulations has...
You could dump many
Just a note regarding the performance issues mentioned. You are
using reaction-field electrostatics case in which by default there is
very little force workload left for the CPU (only the bondeds) and
therefore the CPU idles most of the time. To improve performance, use
-nb gpu_cpu with multiple
ya.. but there is experimental data to confirm the presence. can you help
me to solve this problem
On 9 July 2013 11:54, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Is this, http://en.wikipedia.org/wiki/Xenon, your Xe ? If so, it will
obviously not sit in the binding site
Dr. Vitaly V.
Generally:
Using a higher force constant and / or pulling velocity drives the
system faster out of equilibrium, which results in higher rupture forces.
Varying the force constant has two effects. The softer the potential is,
the larger are the fluctuations in the coordinates but the lower are
On 7/9/13 5:34 PM, Melchor S. wrote:
Sorry for the misunderstanding. I should had explained it better.
I know that is a zwitterionic residue, I have run several simulations with
the same PDB and with other forcefields. ACPYPE does not work, I tried it
yesterday, but I have to check it.
On 7/9/13 7:13 PM, Bin Liu wrote:
Hi All,
For the convenience of visualization, I need to remove the jump of one
component (say a protein) of the system at the boundary. I don't need to,
or say I need not to remove the jump of the other components (say a lipid
bilayer), since otherwise the
On 7/9/13 7:38 PM, rookie417 wrote:
Thanks Justin and Stephan,
One more question, while pulling from the interior of a multiple monomer
micelle structure, I used higher force constants (5000 kJ/mol/nm^2) for
position restraints on the reference group to keep the system intact. I am
assuming
On 7/10/13 3:13 AM, ashish24294 wrote:
I changed the cut-offs as follows, still isn't helping. I tried restraining
the urea which also didn't work. I have attached the topology as well.
topolurea.top
http://gromacs.5086.x6.nabble.com/file/n5009723/topolurea.top
The urea.itp looks
Hi there,
You said ACPYPE didn't work… Can you give details? Have you try with GAFF
first? If you don't mind, can you post me your molecule in private email?
Thanks,
Alan
On 9 July 2013 22:34, Melchor S. msm...@cid.csic.es wrote:
Sorry for the misunderstanding. I should had explained it
Hi Thomas,
thank you for your reply.
Hi Mike,
Your confusion might stem from a very simple issue.
To see the overlap of the forward and backward distributions,
you have to plot
N(+Delta H(lambda=x) | lambda=y) and
N(-Delta H(lambda=y) | lambda=x).
Do I understand it right, that for
Hi,
--
Do I understand it right, that for instance (consider lambda step = 0.5)
ONLY
N(+Delta H(lambda=0) | lambda=0.5) AND N(-Delta H(lambda=0.5) |
lambda=0)
has to overlap, and then
N(+Delta H(lambda=0.5) | lambda=1) AND N(-Delta H(lambda=1) |
lambda=0.5)
has to
Dear Justin
I do your tutorial entitled KALP15 in DPPC .
In Step Three: Defining the Unit Cell Adding Solvent,
You said Use trjconv to remove periodicity .
When I use trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol
-ur compact,
gromacs tell me: Select group for output.
Which
On 7/10/13 8:32 AM, Atila Petrosian wrote:
Dear Justin
I do your tutorial entitled KALP15 in DPPC .
In Step Three: Defining the Unit Cell Adding Solvent,
You said Use trjconv to remove periodicity .
When I use trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol
-ur compact,
Dear users,
I have a few questions about PCA analysis. I see the figures below in the most
of the publications:
1.) Figure:Eigenvalues along the eigenvectors
This figure gives contribution of eigenvalues along the eigenvectors to the
overall motion of the protein???
2.) Figure:the projection of
Dear users,
I extracted separate extreme projections using g_anaeig. I have to make
pictures which show the difference. Can you help me, someone who makes them
using pymol before?
--
Ahmet Yıldırım
--
gmx-users mailing listgmx-users@gromacs.org
Dear Justin
Thanks for your quick reply.
I want to study a system containing DOPC and cholesterol and drug.
I correctly prepared gro files and topology parameters for this system.
I did previous step (Step Two: Modify the Topology) without problem.
I have 2 problems.
1) After I use trjconv
Hi,
For a system with several component in the membrane, I think that
InflateGRO 2 would be more appropriate. See
http://code.google.com/p/inflategro2/ for the code and the related
publication http://pubs.acs.org/doi/full/10.1021/ci3000453
Bests,
Baptiste
2013/7/10 Atila Petrosian
Thanks! Mark.
I got solution to my problem. For my system, setting pinoffset = 0, 16
and pinstride = 1 for two simultaneous simulations gave much
satisfactory performance both for Verlet and Group cutoff-scheme. I
tried it for 4 simultaneous simulations also with pinoffset = 0, 8,
16, 24 and
Dear Baptiste
Very thanks for your reply.
Unfortunately, I have not access to InflateGro2. I encountered with error.
If there are a script for InflateGro2 like InflateGro. please sent me perl
script related to InflateGro2.
Best wishes.
--
gmx-users mailing listgmx-users@gromacs.org
On 7/10/13 10:46 AM, Atila Petrosian wrote:
Dear Baptiste
Very thanks for your reply.
Unfortunately, I have not access to InflateGro2. I encountered with error.
If there are a script for InflateGro2 like InflateGro. please sent me perl
script related to InflateGro2.
It's freely available
Dear users,
I am performing MD simulations of short peptides (from 7 to 45 units) in
implicit solvent. I found quite bizarre results: all peptides unfold after
few picosends, adopting a rather linear conformation until the end of MD,
irrespective of temperature (I performed simulations at 200K,
There vectors. Theres some good older papers explaining the whole thing from Van Gunstern, Berendsen, and some other good ones from de Groot that explain them well and includes combining them with other data analysis types, but I dont remeber the actual publications. A few are in the mid 1990s,
Hi all,
I wonder what could be the cause of such a fatal error when using g_hbond
with -contact option.
The two index group I chose have no overlap, but certain index group pairs
worked while others did not and gave this fatal error.
Thanks,
Yun
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gmx-users mailing list
Program g_hbond, VERSION 4.5.4
Source code file: gmx_hbond.c, line: 823
Fatal error:
No donor atom 5226
On Wed, Jul 10, 2013 at 10:58 AM, yunshi11 . yunsh...@gmail.com wrote:
Hi all,
I wonder what could be the cause of such a fatal error when using g_hbond
with -contact option.
The two
Never mind, everyone. Issue solved by always selecting the smaller index
group first.
On Wed, Jul 10, 2013 at 10:59 AM, yunshi11 . yunsh...@gmail.com wrote:
Program g_hbond, VERSION 4.5.4
Source code file: gmx_hbond.c, line: 823
Fatal error:
No donor atom 5226
On Wed, Jul 10, 2013 at
I figured out by using static libraries.
On 07/10/2013 06:52 AM, Éric Germaneau wrote:
Dear all,
I call cmake the following way and get the error bellow:
CC=mpicc CXX=mpicxx
CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin
\
/lustre/utility/bin/cmake \
Dear all,
Anyone have successfully built the 4.6.3 release using MKL?
I keep getting the following error message:
-- Looking for DftiCreateDescriptor - not found
CMake Error at CMakeLists.txt:1018 (message):
Linking with MKL was requested, but was not successful. The
include
Yes, this is probably caused by a known bug in 4.6 that has been fixed
for a month or two and mentioned in the release notes. Some
work-arounds are suggested here
http://redmine.gromacs.org/issues/1249, but you should probably update
to 4.6.3 :-)
Mark
On Wed, Jul 10, 2013 at 5:43 PM, Cristina
Are you following the advice here?
http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL
On Thu, Jul 11, 2013 at 12:24 AM, Éric Germaneau german...@zoho.com wrote:
Dear all,
Anyone have successfully built the 4.6.3 release using MKL?
I keep getting the following error
Yes, as one can see in my first post.
One thing is I don't know what libraries I need and in which order.
Thanks,
Eric.
On 07/11/2013 06:58 AM, Mark Abraham wrote:
Are you following the advice here?
http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL
On
On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau german...@zoho.com wrote:
Yes, as one can see in my first post.
No, because we can't guess whether your icc is 11 or not. If so, you
have a bunch of stuff that is not required. icc 11 has a magic flag
for using MKL, which GROMACS will use if given
I see.
Thank you.
On 07/11/2013 07:08 AM, Mark Abraham wrote:
On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau german...@zoho.com wrote:
Yes, as one can see in my first post.
No, because we can't guess whether your icc is 11 or not. If so, you
have a bunch of stuff that is not required. icc 11
No problems :-) (For the record, the fact that you had to brute-force
static libraries in another thread does not fill me with confidence
that your compiler is installed correctly. But that is for you to
judge! :-)
On Thu, Jul 11, 2013 at 1:11 AM, Éric Germaneau german...@zoho.com wrote:
I see.
I see.
Thank you.
On 07/11/2013 07:08 AM, Mark Abraham wrote:
On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau german...@zoho.com wrote:
Yes, as one can see in my first post.
No, because we can't guess whether your icc is 11 or not. If so, you
have a bunch of stuff that is not required. icc 11
I have the same feeling too but I'm not in charge of it unfortunately.
Thank you, I appreciate.
On 07/11/2013 07:15 AM, Mark Abraham wrote:
No problems :-) (For the record, the fact that you had to brute-force
static libraries in another thread does not fill me with confidence
that your
VMD might do what you want with the PBC tools plugin (installed by
default). http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
unwrap being the equivalent of -nojump
Otherwise, couldn't you just view your 2 trajectories simultaneously, one
with protein the other not?
-Trayder
On Wed, Jul
Thanks mate, I am trying it now :)
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Trayder Thomas
Sent: Thursday, 11 July 2013 11:52 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to apply trjconv -nojump
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