Hi!
I have problem in running gromacs 4.6 in PBS queue...
I end up with error:
[n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv
failed: Connection reset by peer (104)
--
mpirun noticed that process rank
Hi guys!
Thanks for help!
I have finally manage to solve this problem.
Like Szilárd notice it was a problem with assembler.
When I installed binutils-2.23.1 (previously I had 2.20.1) it worked :)
So my combination was gcc 4.7.2 and binutils-2.23.1.
All the best!
tomek
On Sun, Feb 3, 2013 at
On Sat, Feb 2, 2013 at 12:34 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Sat, Feb 2, 2013 at 1:00 AM, Justin Lemkul jalem...@vt.edu wrote:
On 2/1/13 5:26 PM, didymos wrote:
Hi Justin!
I had the same problem and I used your advise but I am not sure if this
entirely worked
Páll szilard.p...@cbr.su.se wrote:
On Sat, Feb 2, 2013 at 2:38 PM, Tomek Wlodarski
tomek.wlodar...@gmail.comwrote:
On Sat, Feb 2, 2013 at 12:34 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Sat, Feb 2, 2013 at 1:00 AM, Justin Lemkul jalem...@vt.edu wrote:
On 2/1/13 5
On Sat, Feb 2, 2013 at 10:12 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Sat, Feb 2, 2013 at 8:48 PM, Tomek Wlodarski
tomek.wlodar...@gmail.comwrote:
Thanks Szilárd, good idea:)
I tried to build gromacs and I got errors..:
/tmp/ccBvi1my.s: Assembler messages:
/tmp/ccBvi1my.s
On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski
tomek.wlodar...@gmail.com wrote:
Hi Francesco,
Thanks!
However, it does not work with my case..
tomek
On Sun, May 20, 2012 at 1:47 PM, francesco oteri
francesco.ot...@gmail.com wrote:
Hi,
usually I use something like:
mdrun_mpi -v
that it has to load topol_1.cpt
topol_2.cpt ecc.ecc
Anyway, you can do a small test, i.e. using 5 replicas and stopping you
simulation after a few seconds
Francesco
2012/5/20 Tomek Wlodarski tomek.wlodar...@gmail.com
Hi,
I am running REMD simulation:
mdrun_mpi -v -deffnm -s topol_
Hi,
I have notice that quite often people in REMD simulation use replicas in
lower than 300K temp.
Using for example temperature ranges from 250 to 450K
I am wondering what is the purpose of those replicas.
I have limited computational resources and I am wondering if for studing
175 aa protein is
better when you also include lower temperature.?
best!
tomek
On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 27/04/2012 10:59 PM, Tomek Wlodarski wrote:
Hi,
I have notice that quite often people in REMD simulation use replicas in
lower than 300K temp.
Using
Hi,
I would like to simulate protein in DMPC bilayer in Charmm36 ff.
I checked mailing list and KALP-15 tutorial, but still I have a few basic
questions.
1) I have problem with DMPC bilayer...
- VMD membrane builder only provides POPE and POPC lipids...
- on the Peter Tieleman page there is a
Hi Shahid,
Use spc216.gro file, it also works for tip3p water model.
Best!
tomek
On Fri, Dec 16, 2011 at 11:26 AM, shahid nayeem msnay...@gmail.com wrote:
Dear all
I want to use tip3p water model for solvating my protein with genbox command
. I couldnt find tip3p.gro file in
Hi all!
I would like to carry out a simulation of protein with Zn ion
coordinated by 2 Cys and 2 His in Gromos ff.
So I would need a deprotonated Cys however I know that it is present
only in Amber ff...
Do any of You have some experience with deprotonated Cys in Gromos ff?
especially bounded to
!
Best!
tomek
On Fri, May 6, 2011 at 10:28 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hey :)
Option -center shifts the system, which will show up as a component in the
displacement.
Cheers,
Tsjerk
On May 6, 2011 5:39 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Tomek Wlodarski wrote
wrote:
Tomek Wlodarski wrote:
Hi all!
I have a trajectory of simulation (protein in box of water) and I
would like to have all the time protein in the center of the water
box, becasue protein is drifting to the edge during simulation and I
am calculating some properties of water arround
Hi all!
I have a trajectory of simulation (protein in box of water) and I
would like to have all the time protein in the center of the water
box, becasue protein is drifting to the edge during simulation and I
am calculating some properties of water arround the protein.
I was playing with trjconv
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