My problem was here:
>nsteps = 10
which should read
nsteps = 1
I was under the assumption that the step numbers would correspond to the
number of calculated eigenvectors. All eigenvectors are calculated in step
1.
Thanks,
Bryan
On Thu, Apr 11, 2013 at 12:33 PM, David van der Spoel
wrote
Hi Berk and others,
Sorry it has been a long time since this issue was posted, but I got
side-tracked from this issue with other projects. And I want to make sure I
understand this correctly before venturing into more simulations. So this gets
a little long winded, but I hope you will help me f
On 2013-04-11 22:20, Ahmet yıldırım wrote:
could anybody help me please?
Check http://pubs.acs.org/doi/abs/10.1021/ct200731v
2013/4/11 Ahmet yıldırım
Dear users,
I calculated diffusion constant of a substance using g_msd tool. I also
want to calculate thermal conductivity its. By the way
also I found such parameters in the native charm format (.prm)
could you provide me with some script for conversion of tpr to itp? I could
do such topology for cytochrome and add it to the contribution :)
James
2013/4/12 James Starlight
> I forgot to point out that when I made topology for cyt
On Fri, Apr 12, 2013 at 3:45 PM, 라지브간디 wrote:
> Thanks for your answers. I have uninstalled the mpi, have also reinstalled
> the CUDA and got the same issue. As you have mentioned before I noticed that
> it struggle to detect the CUDA.
Do you mean that you reconfigured without MPI and with CUDA
On Fri, Apr 12, 2013 at 5:53 PM, Hua Lu wrote:
> Hi!
> I got the following error message while compiling gromacs using a complete
> installation of Cygwin on 64bit windows 7. Any idea what the problem is?
>
Yes, you can't read those files. We can't know why. You wrote them as a
different user, o
On Fri, 12 Apr 2013, Thomas Evangelidis wrote:
On 12 April 2013 07:51, anu chandra wrote:
Hi David,
Thanks for the reply. I have not tried yet. Since I didn’t find query about
the dihedral PCA in the mail list, I thought of confirm about the steps
mentioned in the web site.
Regarding the u
Hi!
I got the following error message while compiling gromacs using a complete
installation of Cygwin on 64bit windows 7. Any idea what the problem is?
This is what I have used to install as detailed on the gromacs website:
cd gromacs-4.6.1
mkdir build
cd build, cmake .. -DGMX_BUILD_OWN_FFTW=ON
m
Thanks for your answers. I have uninstalled the mpi, have also reinstalled the
CUDA and got the same issue. As you have mentioned before I noticed that it
struggle to detect the CUDA.
Can cygwin recognize the CUDA installed in win 7? if so, how do i link them ?
The default installation path o
Dear All,
During a simulation of a protein with a ligand, I see the -NH3 of the
lysine side chain near the ligand is getting squeezed for a very short
time; N-H bonds are getting contracted and the angle are no longer within
tetrahedral normal http://lists.gromacs.org/pipermail/gmx-users/2010-Nov
Hi Natalia,
I am not aware whether the QM/MM implementation in GROMACS works in 4.6,
nor with which Gaussian version was intended to work in the past. Perhaps
Gerrit Groenhof or someone on gmx-users can update us here?
I'm not sure what "diff file" you are seeking, either. Can you elaborate
pleas
On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen wrote:
> Dear All,
>
> I made a POPC bilayer and carried out embedding a protein into this
> membrane. But the fatal error has appeared :
> Fatal error:
> Something is wrong with your membrane. Max and min z values are 12.342000
> and 0.016000. Mayb
I forgot to point out that when I made topology for cytochrome-HEME complex
( assuming one cysteine covalently bonded to the FE ) again I've forced
with the lack of charmm parameters for such cysteine-HEME interactions (
I've only found it for His coordinating bond).
ERROR 1 [file topol.top, line
Dear All,
I made a POPC bilayer and carried out embedding a protein into this
membrane. But the fatal error has appeared :
Fatal error:
Something is wrong with your membrane. Max and min z values are 12.342000
and 0.016000. Maybe your membrane is not centered in the box, but located
at the box edg
>
> > dPCA is
> > preferred in cases of peptides or intrinsically disordered proteins.
> >
>
> And even then a disordered mess can still be a disordered mess...
>
>
Very true!
--
==
Thomas Evangelidis
PhD student
University o
On Fri, Apr 12, 2013 at 11:28 AM, Thomas Evangelidis wrote:
> On 12 April 2013 07:51, anu chandra wrote:
>
> > Hi David,
> >
> > Thanks for the reply. I have not tried yet. Since I didn’t find query
> about
> > the dihedral PCA in the mail list, I thought of confirm about the steps
> > mentioned
Indeed it's strange. In fact, it seems that CUDA detection did not
even run, there should be a message whether it found the toolkit or
not just before the "Enabling native GPU acceleration" - and the
enabling should not even happen without CUDA detected.
Unrelated, but do you really need MPI with
That looks really strange. CMake claims to detect CUDA but the right
variables are not set.
1) Can you reproduce this in a clean build directory?
2) If so, what CUDA is present?
Mark
On Thu, Apr 11, 2013 at 2:57 PM, 라지브간디 wrote:
> Dear gmx,
>
>
> I have installed mpich for MPI use in cygwin (
Yes, from 4.5.x manual:
pull_ngroups: (1)
The number of pull groups, not including the reference group. [...]
Just set 'pull_ngroups = 2' and then make entries for
pull_group1 -> pull_vec1 ...
pull_group2 -> pull_vec2 ...
and so on...
greetings
thomas
Am 12.04.2013 12:00, schrieb gmx-users-req
On 12 April 2013 07:51, anu chandra wrote:
> Hi David,
>
> Thanks for the reply. I have not tried yet. Since I didn’t find query about
> the dihedral PCA in the mail list, I thought of confirm about the steps
> mentioned in the web site.
>
>
> Regarding the use of dihedral PCA, the protein with w
by the way also I've tried to make model of cytochrome p450 in charmm. In
that case heme have only one coordinate bond with the side chain of
cysteine (not 2 covalent bonds with cysteines as in the cytochrome-C). So
as I understand I should include model of heme as the diffusion ligand ( as
the sep
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