Hi Justin,
Thanks a lot, that suggestion of yours helped. I am on the equilibration
step and its running but nothing is happening on the terminal its just
stagnant. Is it fine because its more than 17 hrs now. Is there some
problem.
After running the second command nothing is happening on the term
>> Date: Fri, 1 Mar 2013 23:59:36 +0530
>> From: "Abhishek Acharya"
>> Subject: [gmx-users] Installation Problems with Gromacs4.6
>> To: "gromacs maillist"
>> Message-ID:
>> <2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in>
>> Content-Type: text/plain;charset=iso-8859-1
>>
>>
> Date: Fri, 1 Mar 2013 23:59:36 +0530
> From: "Abhishek Acharya"
> Subject: [gmx-users] Installation Problems with Gromacs4.6
> To: "gromacs maillist"
> Message-ID:
> <2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hello Gr
On 3/1/13 3:49 PM, Villarealed wrote:
Dear Gromacs-Users,
I am using Gromos96 43a1 FF extended to include phosphorylated residues.
I have a peptide-capped with 17 aminoacids.
When I tried to add ions to the virtual box
I obtained these error
ERROR 1 [file topol.top, line 566]:
No default G9
On Fri, Mar 1, 2013 at 7:29 PM, Abhishek Acharya wrote:
> Hello Gromacs Users.
> I have been trying to install Gromacs4.6 on our HPC facility. I think I
> have correctly provided all the necessary mpi and fftw library paths.
OK, but you'll make trouble-shooting easier if you tell us what you've
Dear Gromacs-Users,
I am using Gromos96 43a1 FF extended to include phosphorylated residues.
I have a peptide-capped with 17 aminoacids.
When I tried to add ions to the virtual box
I obtained these error
ERROR 1 [file topol.top, line 566]:
No default G96Angle types
ERROR 2 [file topol.top, line
The easiest way for solution is to kill MacOS ans switch to Linux.
;-)
Albert
On 03/01/2013 06:03 PM, Szilárd Páll wrote:
Hi George,
As I said before, that just means that most probably the GPU driver is not
compatible with the CUDA runtime (libcudart) that you installed with the
CUDA toolki
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think I
have correctly provided all the necessary mpi and fftw library paths. But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find
Hi Erik,
Since I read in the mailing list that nobody had asked about 2.1.0, just
decided to try an older version before going into the trouble itself...
Kind of coward, I know, but the troubles with that version are already
reported so that I thought things would be easier :)
Thank-you a lot for
Interesting. Perhaps there are new issues with 2.1.0. Did you try to
execute the command yourself?
Erik
On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote:
The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and
it works
fine. However, when converting the xpm to eps I
Hi George,
As I said before, that just means that most probably the GPU driver is not
compatible with the CUDA runtime (libcudart) that you installed with the
CUDA toolkit. I've no clue about the Mac OS installers and releases, you'll
have to do the research on that. Let us know if you have furthe
On 3/1/13 11:16 AM, Miguel Ángel Mompeán García wrote:
The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works
fine. However, when converting the xpm to eps I get I plot very small,
where one barely can see the colour code and the legend is sooo big. Does
anyone know how to
The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works
fine. However, when converting the xpm to eps I get I plot very small,
where one barely can see the colour code and the legend is sooo big. Does
anyone know how to change that?
2013/3/1 Erik Marklund
> What happens i
Hi,
Then the problem lies in automating what molecules are to be removed,
right? Try g_select or look into trjorder.
Erik
On Mar 1, 2013, at 2:45 PM, gromacs query wrote:
Aha! thanks Erik (and Justin),
I really feel sorry 35 and 135 will be removed by sed. I must have
given a
thought ab
Hi Stephen,
computing errors from umbrella sampling is not trivial at al.
Generally, there are two possibilities:
- If each histogram overlaps only with one neighboring histogram, you
*must* know the autocorrelation time of each window. This is often a
problem in MD simulations, because there
Dear gromacs users,
I am performing united atom simulations of a hydrophobic drug and its ligand
with 53a6 ff. Should I instead choose an all atom force field in order to
reproduce all the protein-drug interactions for accuracy?
Thank you in advance.
Regards,
Revathi
--
gmx-users mailing list
Hi everyone!
I want to add the distance restraint for some atom pairs. However, it is not
working at all. The yielded bond length can easily go beyond 0.5~0.6 nm. Has
anyone got a hint? Thanks very much!
[ distance_restraints]
; ai aj type index type' low up1 up2 fac
157910
Hi,
Now I've tested the version of g_current in 4.6 and for me it works fine.
/Flo
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] Im Auftrag von Florian Dommert
> Gesendet: Mittwoch, 27. Februar 2013 18:46
> An: 'Discussion list
Hi Szilαrd
Thanks for your reply. I have run the deviceQuery utility and what I got
back is
/deviceQuery Starting...
CUDA Device Query (Runtime API) version (CUDART static linking)
cudaGetDeviceCount returned 38
-> no CUDA-capable device is detected
Should I understand from this that the CUDA
Aha! thanks Erik (and Justin),
I really feel sorry 35 and 135 will be removed by sed. I must have given a
thought about that. So this was reason sed was over doing the things. Also
as you asked: They are random residue number water molecules so
not continuous and they were selected on the criteria
On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
Dear Erik,
so you can filter out the unwanted residues there instead of
using an
index file.
There are thousands of water to be removed so simple commands like
sed
exhausts when I run it
On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
Dear Erik,
so you can filter out the unwanted residues there instead of using
an
index file.
There are thousands of water to be removed so simple commands like sed
exhausts when I run it in loops. e.g. Just to say :
sed -e '/35SOL/d' -e '/3
On 3/1/13 7:47 AM, zhhxu wrote:
Dear Justin:
Thank you for reply. g_x2top worked correct as you suggested when I added
"-nopbc" option.
I have other questions about graphite simulation. The top/rtp file(opls-aa)
generated by g_x2top missed improper dihedral term ,
to keep a carbon in
On 3/1/13 7:58 AM, gromacs query wrote:
Dear Erik,
so you can filter out the unwanted residues there instead of using an
index file.
There are thousands of water to be removed so simple commands like sed
exhausts when I run it in loops. e.g. Just to say :
sed -e '/35SOL/d' -e '/36SOL/d'
Dear Erik,
>> so you can filter out the unwanted residues there instead of using an
index file.
There are thousands of water to be removed so simple commands like sed
exhausts when I run it in loops. e.g. Just to say :
sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/40SOL/d'
-e
What happens if you execute the command (/usr/local/bin/dssp/ -i
ddQ3PqtX -o ddR1HavD) in your terminal?
Erik
On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error
you got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3Pqt
The ndx format is really simple. You can easily script your way to a
new index group as long as the selection of atoms can be automated.
Furthermore, the gro format is also simple, so you can filter out the
unwanted residues there instead of using an index file.
Erik
On Mar 1, 2013, at 1:4
Dear Justin:
Thank you for reply. g_x2top worked correct as you suggested when I added
"-nopbc" option.
I have other questions about graphite simulation. The top/rtp file(opls-aa)
generated by g_x2top missed improper dihedral term ,
to keep a carbon in plane, whether it is better to add t
Dear All,
I know the residue numbers of SOL molecules (which are more than thousands)
which I want to remove them from a gro file. I searched that make_ndx can
be used make a index file to define residues. But It is a prompt based tool
and its difficult to type manually thousands of residue number
With -ver, just like it says. do_dssp -h explains how. What dssp
version do you have?
Erik
On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error
you got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /de
Dear gmx users,
Has anyone tried dssp-2.1.0 with gromacs-4.6?
I am having the common problems that were supossed not to be in the new
releases
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I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
/dev/null'
Reading frame 0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#
---
HI,
That looks like the driver does not work or is incompatible with the
runtime. Please get the SDK, compile a simple program, e.g. deviceQuery and
see if that works (I suspect that it won't).
Regarding your machines, just FYI, the Quadro 4000 is a pretty slow card
(somewhat slower than a GTX 46
Thanks Justin and Kukol for the info.
Kukol, Can you please upload the cholesterol parameters also in the site
you provided, if you have??.
On Fri, Mar 1, 2013 at 2:02 PM, Kukol, Andreas wrote:
> Hello Venkat,
>
> You can use Gromos96 53a6 lipid parameters for DPPC, DMPC, POPC and POPG
> with t
On 3/1/13 2:54 AM, Ashalatha Sreshty wrote:
Dear Justin,
I did the same before but didnot get the eigenvectors. I am working on
Gromacs-4.5.4.
The actual command line used is as below
g_anaeig_d -f mlecdig-MD-0-202-noPBC.xtc -s mlecdig-MD-1.tpr -v
eigenvec-mlecdig-2-102.trr -eig eigenval-mle
https://mcule.com/apps/1-click-docking/
On 03/01/2013 11:03 AM, James Starlight wrote:
Dear Gromacs Users!
During preparation of the protein-ligand complex (manual placement of
the ligand into the ligand-binding pocket (based onto known x-ray
data) I've forced with the overlap of some polar si
Dear Gromacs Users!
During preparation of the protein-ligand complex (manual placement of
the ligand into the ligand-binding pocket (based onto known x-ray
data) I've forced with the overlap of some polar sidechains of the
ligand interiour with big aromatic group of the ligand itself. I've
tried
Hello Venkat,
You can use Gromos96 53a6 lipid parameters for DPPC, DMPC, POPC and POPG with
the Gromos96 53a6 force field.
They can be downloaded from here:
https://sites.google.com/site/bioherts/home/lipid-topologies
Reference:
Kukol, A., 2009. Lipid models for united-atom molecular dynamics
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