Hi all,
I tried to make an account on http://redmine.gromacs.org/ by filling the
online form, but didn't receive any E-mail of confirmation. When I try
to register again, it tells me my E-mail is already used, but when I ask
for a forgotten passwd it tells me my E-mail doesn't correspond to any
On Mon, Dec 9, 2013 at 1:44 AM, Michael Shirts wrote:
> So, I'm trying to compile with MPI using mpich3. Previous
> installations worked, and installations without MPI worked. I'm
> getting errors like:
>
> /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53:
> warning: parameter
Do your tabulated functions work on a toy system, like butane?
On Dec 9, 2013 6:47 PM, "Chandan Choudhury" wrote:
> I am facing some weird problem while using tabulated potentials (esp.
> dihedral tabulated potentials) in gromacs 4.6.3. I am trying to generate a
> coarse grained (CG) trajectory u
On Mon, Dec 9, 2013 at 5:41 PM, Mark Abraham wrote:
> Do your tabulated functions work on a toy system, like butane?
>
No Mark. I didnot try with butane. The simulation stops when I incorporated
tabulated dihedral potential.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
Gromacs Users m
On 12/9/13 8:09 AM, Chandan Choudhury wrote:
On Mon, Dec 9, 2013 at 5:41 PM, Mark Abraham wrote:
Do your tabulated functions work on a toy system, like butane?
No Mark. I didnot try with butane. The simulation stops when I incorporated
tabulated dihedral potential.
Which is precisely why
Hi,
Please let me know whether the below issue (link) has been addressed in
this release:
http://bugzilla.gromacs.org/issues/1340
If no then is there any plan to include this in future release.
--
*Thanks and Regards,Bipin Singh*
--
Gromacs Users mailing list
* Please
On Mon, Dec 9, 2013 at 6:46 PM, Justin Lemkul wrote:
>
>
> On 12/9/13 8:09 AM, Chandan Choudhury wrote:
>
>> On Mon, Dec 9, 2013 at 5:41 PM, Mark Abraham
>> wrote:
>>
>> Do your tabulated functions work on a toy system, like butane?
>>>
>>> No Mark. I didnot try with butane. The simulation sto
There's two issues here; an actual bug (#1315) with intramolecular 1-4
interactions when combining function type 2 and 1, and the fact that
couple-intramol doesn't do exactly what you might expect it to do,
i.e.: right now, if one sets coupl-intramol = yes, LJ and Coul 1-4's
are left on (uncoupled)
Dear all,
I originally posted this a couple of weeks ago, but haven't had much luck
fixing in myself or finding a solution from the forums or elsewhere so I'm
re-posting it in the hope someone will have an idea. Apologies for posting
multiple times.
Originally I tried to extend a protein simulati
Thank You Prof. Shirts for your clarification.
On Mon, Dec 9, 2013 at 9:40 PM, Michael Shirts wrote:
> There's two issues here; an actual bug (#1315) with intramolecular 1-4
> interactions when combining function type 2 and 1, and the fact that
> couple-intramol doesn't do exactly what you migh
Hi all,
I have a physical compute node with 2x 6-core Intel E5649 processors +
three NVIDIA Tesla M2070s GPUs.
First I tried using all 12 CPU cores + 3 GPUs for an equilibration run (of
protein in TIP3 waters), which gave me 8.964 ns/day performance.
But I noticed the PME mesh calculation, which
On 2013-12-09 18:27, yunshi11 . wrote:
Hi all,
I have a physical compute node with 2x 6-core Intel E5649 processors +
three NVIDIA Tesla M2070s GPUs.
First I tried using all 12 CPU cores + 3 GPUs for an equilibration run (of
protein in TIP3 waters), which gave me 8.964 ns/day performance.
But
Hi David,
On Mon, Dec 9, 2013 at 9:40 AM, David van der Spoel wrote:
> On 2013-12-09 18:27, yunshi11 . wrote:
>
>> Hi all,
>>
>> I have a physical compute node with 2x 6-core Intel E5649 processors +
>> three NVIDIA Tesla M2070s GPUs.
>>
>> First I tried using all 12 CPU cores + 3 GPUs for an eq
Hello:
I am calculating the water density inside my membrane protein along Z
directions. I used the a_ri3DC tool in Gridcount which is a patch in
Gromacs for calculation:
a_ri3Dc -grid gridxdr.dat -profile profile.xvg -xyp xyp.dat -xzp xzp.dat
-yzp yzp.dat -rzp rzp.dat -rdf rdf.xvg -zdf zdf.
Thanks Justin.
I added the bond description in the ffbonded.itp but it does not show in the
topol.top file.
In ffbonded.itp we have:
[ bondtypes ]
; ij func b0 kb
OWHW 10.09572 502080.0 ; For TIP4F Water - wlj 1/98
OWLP 10.01750 753120.0
Hi,
sorry we had a mixup with the account activation. Your account should be
activated now.
Roland
On Mon, Dec 9, 2013 at 3:35 AM, Patrick Fuchs <
patrick.fu...@univ-paris-diderot.fr> wrote:
> Hi all,
> I tried to make an account on http://redmine.gromacs.org/ by filling the
> online form, but
Hi,
That looks suspiciously like a bug, perhaps of the same type as 1174.
Please do open a new issue on Redmine, with the above content, so that your
report does not get lost. If you are able to do cmake
-DCMAKE_BUILD_TYPE=RelWithDebInfo and run with that mdrun, then the above
stack trace should h
Hi,
Sorry, I don't remember the observation that led to my statement, but I
believed it to be true and since pretty much none of the developers still
use particle decomposition, nobody has corrected me! Your observations
suggest that checkpointing is working fine for you. You should be able to
pro
Dear Users:
Does anybody know how to set the B-state values for position restraints?
I ask because I'm doing FEP of one part of the system, but I want to keep
absolute position restraints on a different part of the system.
What I want to do is like this:
free-energy = yes
init-lambda = 0
coupl
Thanks for your reply.
I have a paracetamol crystal and I would like to estimate the
paracetamol/paracetamol interaction per unitcell.
To do this I am doing the following:
Energy of interaction of paracetamols per unitcell=
Energy of a unitcell - (Energy of a molecule in the unitcell* number
Dear All,
Is it possible to do pressure based replica exchange simulations in gromacs?
Basically I want to do replica exchange simulations for my membrane system at
different surface tensions. If I just set different pressures in the mpd file,
then the mdrun will complain "systems are all the s
On 2013-12-10 02:40, Golshan Hejazi wrote:
Thanks for your reply.
I have a paracetamol crystal and I would like to estimate the
paracetamol/paracetamol interaction per unitcell.
To do this I am doing the following:
Energy of interaction of paracetamols per unitcell=
Energy of a unitcell - (En
22 matches
Mail list logo
