> I am (trying to be) a new user of gromax, but when I do:
> ./configure CC=gcc34
Did you try to execute just
./configure ?
I think it should help if your linux version is quite up-to-date.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svobody sq.,4, Kharkiv 61077, Ukra
I see no problems to use gromacs for it. You make find the parameters
in /top/ions.itp (include ions.itp to your topology) in your gromacs directory.
Then you can use 'genconf' to create a system of the desired size.
> hi gmx users,
> Can Gromacs be used to simulate NaCl crystallization a
rams rams wrote:
Hi,
I have three di sulphide bonds in my crystal structure. In the
topology file it left blanks at the corresponding sulphur
connectivities (i.e., values corresponding to gb_, ga_. gd_ ). When I
try to create the .tpr file it complains the following:
processing topology..
Hi,
I have three di sulphide bonds in my crystal structure. In the topology file
it left blanks at the corresponding sulphur connectivities (i.e., values
corresponding to gb_, ga_. gd_ ). When I try to create the .tpr file it
complains the following:
processing topology...
Generated 716 of the 26
when using the default gcc 4.1.0 I got the same error. I went to gcc 3.4
because I read that version 4 had problems.
there is a link in /lib/cpp to /usr/bin/cpp
maxi
On Sat, 2008-06-28 at 00:21 +0300, Jussi Lehtola wrote:
> On Fri, 2008-06-27 at 16:50 -0300, Maximiliano A. Burgos Paci wrote:
>
Why do you want to use GCC 3.4 instead of the default compiler of the
distribution which is GCC 4.1.2 invoked with gcc?
From the Downloads section of the home page:
"WARNING: do not use the gcc 4.1.x set of compilers. They are broken.
These compilers come with recent Linux distrubutions li
On Fri, 2008-06-27 at 16:50 -0300, Maximiliano A. Burgos Paci wrote:
> I am (trying to be) a new user of gromax, but when I do:
> ./configure CC=gcc34
>
> I get :
>
> configure: error: C preprocessor "/lib/cpp" fails sanity check
>
> I have a Fedora Core 7 i386 system. gcc version 3.4.4 2005072
hi gmx users,
Can Gromacs be used to simulate NaCl crystallization and melting?
If it could, where can I find pdb/top/itp etc. input files? Thanks in
advance.
Best regards,
William
___
gmx-users mailing listgmx-users@gromacs.org
http://www.g
I am (trying to be) a new user of gromax, but when I do:
./configure CC=gcc34
I get :
configure: error: C preprocessor "/lib/cpp" fails sanity check
I have a Fedora Core 7 i386 system. gcc version 3.4.4 20050721.
Could someone help me?
Thanks in advance.
Maxi
__
Many people use the DPPC structure and topology found here:
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
-Justin
Jennifer Johnston wrote:
Does anyone have a DPPC bilayer (any size is fine)? or a topology/gro
for DPPC (either single or bilayer) that they can let me use?
Does anyone have a DPPC bilayer (any size is fine)? or a topology/gro
for DPPC (either single or bilayer) that they can let me use?
Many thanks,
Jen
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Out of curiosity, what version of Gromacs are you using? Did you
compile it from source? If so, which compiler versions (most
importantly, gcc)?
I had a problem with a broken Ubuntu package (GMX 3.3.1) that gave
similar strange behavior. It's a long-shot, but a broken installation
can resu
Well, the way you should follow depends much on what you want to
calculate exactly.
Of course, any artificial constraint is bad.
> It is even worst! Removing the center of mass motion of your protein
> alone as suggested is an aberration and should never be done!
> That doesn't necessarily "fix"
While the frequency with which this question is asked does of course
say something about how diligently some users are searching the list
archives and using the wiki before posting a question, it remains true
that this is causing headaches for a significant number of new users.
I therefore
> I am very new to Gromacs and I am really really running into problems while
>setting up the input file for insulin simulations. Are there any one who
> had
>bit experience in handling insulin (both the chains) ?
And if so, what? I do not see your question here.
--
Vitaly V. Chaban
Scho
Hi
I am very new to Gromacs and I am really really running into problems while
setting up the input file for insulin simulations. Are there any one who
had
bit experience in handling insulin (both the chains) ?
___
gmx-users mailing listgmx-use
Hi ,
When I run tpbconv command for extending run its adding high number of
steps rather than I need,
The command line is
*tpbconv -f .trr -s .tpr -e .edr -o out.tpr -extend 1000
it has run without error at final lines it showed that
Extending remaining runtime of by 1000 ps (now 550 st
Hi Users,
I have run the protein simulation for 9ns, with 1ns each time by using
tpbconv *command, after converting all9ns .trr files to .xtc i have deleted all
.trr files. Later I have catenated all the 9ns simulation files by using trjcat
command. Now I want restart my simulation, so
I think Bhanu was embarrassed that one part of his protein was from one side
and the
remainder was from another. Of course, there cannot be a state
'outside' in reality.
TW> Whatever the case, everyone doing MD simulations should be aware of
TW> periodic boundary conditions. There is no "outside
On Fri, 27 Jun 2008 13:28:18 +0200
"Tsjerk Wassenaar" <[EMAIL PROTECTED]> wrote:
Hi,
That doesn't necessarily "fix" the "problem".
It is even worst! Removing the center of mass motion of your protein
alone as suggested is an aberration and should never be done!
Which position of the
protein
Hi,
That doesn't necessarily "fix" the "problem". Which position of the
protein is taken as a reference depends on the position of the first
atom. Gromacs wants to have the first atom of a molecule in the
rectangular unit cell at the origin. Even if you set comm removal for
the group, the initial
> am new to Gromacs. I tried a 10 ps simulation with a protein and after the
> run, the protein came out of the box.. is it good or bad?
Its terrible. If it runs away you'll never have a new such frolicsome
protein... ;)
> How can I keep the protein in the box?
Just fix it. In .mdp file write co
Hi,
I have never heard of GROMOS 53b6. Does it exist?
The only "vacuum" GROMOS force field I know of is 43b1.
I just removed 43b1 from Gromacs, since it is not at all a vacuum force field.
It was intended to simulate solvated protein with implicit solvent.
Effectively the only change was that cha
Browse the archives, check the wiki.
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
Tsjerk
On Fri, Jun 27, 2008 at 8:06 AM, Bhanu <[EMAIL PROTECTED]> wrote:
> Hi all,
> am new to Gromacs. I tried a 10 ps simulation with a protein and after the
> run, the protein came out of the bo
If you want to keep any group planar during MD you can try to define improper
dihedrals in your topology file.
See the manual, ff*.rtp and ff*bon.itp files.
-Original Message-
From: Abu Naser <[EMAIL PROTECTED]>
To:
Date: Thu, 26 Jun 2008 15:46:36 +
Subject: [gmx-users] keeping 4 ato
I think so too. It's a system-specific problem.
The Benchmark runs and finish with the following:
NODE (s) Real (s) (%)
Time:782.000782.000100.0
13:02
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 56.745
26 matches
Mail list logo
