wait for gromacs 4.0.
Yang Ye
Jayant James Jayasundar wrote:
hi all
IS it possible to enable threads in gromacs during configuration?
Thanks
Jayant
Jayasundar Jayant James
Postdoc,
Department of Veterinary and Comparative Anatomy, Pharmacology
and Physiology(VCAPP), Washington state universi
Date: Thu, 01 Jun 2006 15:34:14 +0530
From: "lalitha selvam" <[EMAIL PROTECTED]>
Subject: [gmx-users] freeenergy calculation
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; format=flowed
i have completed my simulation.i want to analyse my protein.can u help me
Hi all. :)
Last message today. It seems that I succeded in switching all "invsqrt"
functins to a new "gmx_invsqrt". Just 57 in the 12 files below:
***
include/vec.h
src/mdlib/csettle.c
src/mdlib/vsite.c
src/mdlib/clincs.c
src
Hi all.
On 6/1/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
> Trying withou the "-ipo" flag now. It still yelds the same weird warning
> (warning #147: declaration is incompatible with "double invsqrt(double)"> (declared at line 565 of "/usr/local/intel/include/math.h")rename all gromacs inv
Hi all!.
First, sorry for the delay in getting in touch again. Bureaucracy. :P
Second, thanks a lot for everybody for advising on this subject. It's helping me a lot to solve this! :)
Anyway, here is where I'm now:
Erik: I'm sure about the flags. Not using the ones for SSE3, despite my
Jianwei Wang wrote:
Hello,
This has something to do with exclusion list.
I have a special need and have to turn 1-3 interactions on, that is, I
need nobonded interactions (vwd and electrostatic) included in energy
calculations for atoms more than one bond away. I have tried the
following, se
Hello,
This has something to do with exclusion list.
I have a special need and have to turn 1-3 interactions on, that is, I
need nobonded interactions (vwd and electrostatic) included in energy
calculations for atoms more than one bond away. I have tried the
following, seems gmx still exclude
Dear GRMxers:
We need some help in running our Gromacs 3.2.1 parallel environment
in 5 nodes of SunFires V20v (dual-core Opteron 2.2, 4 GB DDR2 RAM), gigabit
eth, mpich-1.2.7, using Sun Grid Engine 6.0.
In a 2 processors job (single node), the results are O.K. but in a 4, 6 or 8
proce
Hello,
Can anyone describe the general procedure for SMD in GROMACS? (i.e. how
you designate which atoms are to be pulled, in what direction, and by
what force).
Thanks,
Arneh
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Hi Natalia,
Download Xmgrace from this place and install the rpm.
http://rpmfind.net/linux/RPM/suse/9.0/i386/suse/i586/
xmgrace-5.1.12-112.i586.html
While installing the rpm if you get an error, further Scrolling down
the page u will see links to the requirements for this to
install...fro
Try installing VMD, this software is nice to inspect molecular dynamics
results with gromacs.
Good luck
Cesar
Zakharova, Natalia Leonidovna escribió:
Dear GROMACS community,
I am new to Linux and GROMACS.
I successfully installed Gromacs on TopologiLinux. I can run the
examples in tutoria
You'll want to look up redirection operators for whatever shell
you're using, but here are a couple suggestions:
grompp (usual args) >& file.dat
- or -
grompp (usual args) 2> file.dat
--Tom
On Jun 1, 2006, at 2:36 PM, David Mobley wrote:
So, this is probably a stupid question, but for som
David Mobley wrote:
So, this is probably a stupid question, but for some reason I can't
figure out how to do it...
I need to run a ton of small MD jobs for a whole bunch of different
small molecules, some few of which have errors in their topologies
which cause grompp to fail with an error. Ther
Zakharova, Natalia Leonidovna wrote:
Dear GROMACS community,
I am new to Linux and GROMACS.
I successfully installed Gromacs on TopologiLinux. I can run the
examples in tutorial folder without problems, but I can't look on
any graphic output because I don't have "xmgrace" installed. I did s
So, this is probably a stupid question, but for some reason I can't
figure out how to do it...
I need to run a ton of small MD jobs for a whole bunch of different
small molecules, some few of which have errors in their topologies
which cause grompp to fail with an error. Therefore, I need some
au
Dear GROMACS community,
I am new to Linux and GROMACS.
I successfully installed Gromacs on
TopologiLinux. I can run the examples in tutorial folder without problems,
but I can't look on any graphic output because I don't have "xmgrace"
installed. I did some Internet searches and was able to
Jayant James Jayasundar wrote:
hi all
IS it possible to enable threads in gromacs during configuration?
Thanks
Jayant
no, and it won't help in anyway because nothing has been implemented in
3.3 yet.
Jayasundar Jayant James
Postdoc,
Department of Veterinary and Comparative Anatomy, Pharmacology
hi all
IS it possible to enable threads in gromacs during configuration?
Thanks
Jayant
Jayasundar Jayant James
Postdoc,
Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA.
http://www.chick.com/reading/tr
I have the same problem. Any suggestion??? DSSP
variable is setup correctly, but nothing happens when I run do_dssp. It just
freeze as Elena described.
Thanks in advance,
César.-
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i have completed my simulation.i want to analyse my protein.can u help me
how to calculate the free binding energy calculation,which program i should
use.i've read gromacs manual 3.3 but i'm in need of any other new analysis
are included in version 3.3 or not.so where can i getthe information on
Hi,
concept of 'molecules' as it is applied within Gromacs has been discussed
several times already, also with regards to distance restraints, which can
not be defined between different 'molecules'. Of course you can define
distance restraints between 'real' molecules by having the molecules
with
karamyog singh wrote:
I request you to see section 5.3.3 . Under the [ atomtypes ] section
displayed over there I want to replace c6 and c12 by buckingham
potential. I want to replace O-O LJ interaction with O-O Buckingham
interaction.
Just below that the manual shows [ nonbond_params ] wher
I request you to see section 5.3.3 . Under the [ atomtypes ]
section displayed over there I want to replace c6 and c12 by buckingham
potential. I want to replace O-O LJ interaction with O-O Buckingham
interaction.
Just below that the manual shows [ nonbond_params ] where I think I can
change the
> While running a MD of PE with position restrain, i get this error message
>
> Fatal error: [ file "posre.itp", line 6 ]:
> Atom index (101) in position_restraints out of bounds (1-12)
>
> My atom index goes up to 6000, why do I have to be in the 1-12 range?
< Regards
>
> Alessan
karamyog singh wrote:
Is it not possible to use Buckingham potential instead of default LJ
potential for interaction between same atoms?
Read the manual. Section 4.1 would be a good start.
Mark
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Is it not possible to use Buckingham potential instead of default LJ potential for interaction between same atoms?
Thanks in advance.
-
Karamyog.
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Please
Hi Jones,There are two things I can think of immediately:1. Make sure to set optimization and architecture options for portable code. By default, the intel compiler might generate binaries that use SSE3-specific stuff, although it is unlikely in this part of the code.2. Try setting "CC_FOR_BUILD=gc
make[3]: ** [grompp] Erro 1
make[3]: Leaving directory
`/home/johannes/src/gromacs/gromacs-3.3/src/kernel'
make[2]: ** [all-recursive] Erro 1
make[2]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src'
make[1]: ** [all] Erro 2
make[1]: Leaving directory `/home/johannes/src/gromacs/
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