Dear all,
Is there a way to impart a constant velocity to a group
during a simulation. That is irrespective of any interaction the
velocity will remain same during the course of the simulation.
--
Avinash Kumar.
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gmx-users mailing list
Hi Tsjerk,
I have been thinking about this way, but I do not think have parameters
for C(-dum)-C to C-C-C, for example, the distance between the 1st and
3rd carbons.
thanks
Qiang
Tsjerk Wassenaar wrote:
Hi Qiang,
Couldn't you do it by shortening the chain, turning on/off one of the
CH2 g
wk yeo wrote:
Hello, all,
It is quite common to encounter protein structures in PDB which consist of only the catalytic domain (versus the structure of the entire protein). One such example is: http://www.pdb.org/pdb/explore.do?structureId=1H1W
My questions:
1) Is it a good idea to use such
Hello, all,
It is quite common to encounter protein structures in PDB which consist of only
the catalytic domain (versus the structure of the entire protein). One such
example is: http://www.pdb.org/pdb/explore.do?structureId=1H1W
My questions:
1) Is it a good idea to use such catalytic domai
Gerrit Groenhof wrote:
Type: text/plain; charset="iso-8859-1"
Is there an implementation in gromacs for using a uniform neutralizing
plasma with PME, to avoid use of counterions?
Thank you
-Himanshu
Neutralization is done implicitly, by omitting out the zeroth plane
wavevector (m=0, s
Type: text/plain; charset="iso-8859-1"
Is there an implementation in gromacs for using a uniform neutralizing
plasma with PME, to avoid use of counterions?
Thank you
-Himanshu
Neutralization is done implicitly, by omitting out the zeroth plane
wavevector (m=0, see sec. 4.6 of the gmx m
The only Error message I can find is the rather cryptic::
NOTE: Turning on dynamic load balancing
_pmii_daemon(SIGCHLD): PE 4 exit signal Killed
[NID 1412]Apid 159787: initiated application termination
There are no error's apart from that.
This may not be very helpful, but I googled this particu
If you are using the GROMOS96, the forcefield files are ffG.*. ffgmx are
for the GROMACS forcefield (that is deprecated). The forcefield file titles
are listed in the file FF.dat in the gromacs topology directory. Here are
the contents of my FF.dat file:
11
ffG43a1 GROMOS96 43a1 force fiel
If you are doing simulated annealing, your system explode if you are heating
all the system (protein and water). Divide your system in protein and water
and heat only the protein.
--
From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]>
Sent: Monday, Septe
Hi,
You really do not have any error or warning messages at the end of your log
file, stdlog or stderr?
Up to now there has been only one report of problems.
This is on a cray xt4, where some dlb jobs (with initial empty cells)
stop at step 10 with the error message that some cell dimensions have
Anyone?
On Sat, Sep 27, 2008 at 1:50 AM, Tiago Marques <[EMAIL PROTECTED]> wrote:
> Hello.
>
> Is any work being done to have GROMACS compute on GPUs?
>
> I'm interested in performing research in this area.
>
> Best regards,
>
> Tiago Marques
>
___
I am running some annealing trials on a Cray XT4. And although the
throughput is impressive, I have severe difficulties with stability of
the code.
For my relatively small system of ~7500 atoms the engine typically crash
after ~500k steps.
I am using the bleeding-edge CVS version: mdrun.c (1.141)
Is there an implementation in gromacs for using a uniform neutralizing
plasma with PME, to avoid use of counterions?
Thank you
-Himanshu
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Hi!
I see that you still can scale a lot more than me. Can you, or someone, give
me one of those testes? I would like to compare with a similar machine,
where gromacs is scaling more than one node well.
Best regards,
Tiago Marques
On Thu, Sep 25, 2008 at 2:52 PM, vivek
Hi Qiang,
Couldn't you do it by shortening the chain, turning on/off one of the
CH2 groups? You only have to mind perturbing the bonding and such in
the right way then.
Cheers,
Tsjerk
On Sat, Sep 27, 2008 at 6:32 PM, friendli <[EMAIL PROTECTED]> wrote:
> Dear all,
>
> I have a mutation free ene
Hi
On Sun, Sep 28, 2008 at 6:39 ALin,
That's not really necessary, the tetrahedral geometry is kept by the
angles. It only needs to be imposed in the case of a CHXYZ group with
united atoms.
Cheers,
Tsjerk
M, Chih-Ying Lin <[EMAIL PROTECTED]> wrote:
>
> Hi
>
> I found this improper dihedral a
Minnale,
> Thanks for the reply, what may be the reason GROMACS became great?
Check the JCC 2005 paper: http://www.ncbi.nlm.nih.gov/pubmed/16211538
> sometimes though system explodes it will generate energy minimisation
> output.gro file we cant use this file for further run?
Need more inform
Hi Lin,
>From the amount of questions you pose on the user list and the
unfamiliarity you display with Gromacs/MD basics, it seems that you're
not as experienced with 1. MD, 2. Gromacs and 3. Force fields as you
should be when you modify parameters. That's an experienced-level
topic on which you c
Hi Lin,
That tutorial doesn't really give a good procedure for production work
simulations. Use a rhombic dodecahedron instead, with a distance to
the wall (-d) of at least 1 nm. Maybe it's better to try the tutorial
I put up on http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ It's not
as good on
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