Hi Carlo,
I think I know now what the problem is. The CUDA compiler, nvcc, uses a the
host compiler to compile CPU code which is generated as C++ and therefore,
a C++ compiler is needed. However, up until CUDA 5.0 nvcc did not recognize
the Intel C++ compiler (icpc) and it would only accept icc as
On 12/4/12 4:15 PM, mohammad agha wrote:
Dear Justin,
Thank you very much from your response.
It means that this problem is not important. Should I use -reprod option in
running of md.mdp? I want to obtain micelles as monodisperse with identical
Nagg(aggregation number) in the one simulation
Dear Justin,
Thank you very much from your response.
It means that this problem is not important. Should I use -reprod option in
running of md.mdp? I want to obtain micelles as monodisperse with identical
Nagg(aggregation number) in the one simulation, but distribution of sizes is
broad and it
On 12/4/12 3:57 PM, mohammad agha wrote:
Dear Gromacs Specialists,
I ran one system (to create of micelles) tow times. Time of creation of
micelles was different in each run and for example if it has been created 5
micelles (in the end of simulation) in both of them but the number of molecul
Dear Gromacs Specialists,
I ran one system (to create of micelles) tow times. Time of creation of
micelles was different in each run and for example if it has been created 5
micelles (in the end of simulation) in both of them but the number of molecules
presence in micelles (aggregation number)
On 12/4/12 1:20 PM, venkatesh s wrote:
Respected Gromacs Peoples,
i got following error in the step mdrun nvt
1 particles communicated to PME node 1 are more than 2/3
times the cut-off out of the domain decomposition cell of their charge
group in dimension
On 12/4/12 1:37 PM, Marcelo Depolo wrote:
Hi everyone!
I'm running a protein-ligand simulation and i'm having a little problem
with the ligand atoms coordinates. After I equilibrate the simulation box
with counter-ions, i checked my ligand with VMD and it was ok. After a
minimization process,
Dear Szilárd,
My cmake version in the 2.8.9. The error is
Linking C shared library libgmx.dylib
Undefined symbols for architecture x86_64:
"std::terminate()", referenced from:
do_memtest(unsigned int, int, int) in
libgpu_utils.a(gpu_utils_generated_gpu_utils.cu.o)
memtestState::alloca
On Tue, Dec 4, 2012 at 5:09 PM, Mark Abraham wrote:
> 2fs is normally considered too large a time step for stable integration
> with only bonds to hydrogen constrained, so your observation of
> non-reproducible LINCS warnings is not indicative of some other problem.
>
> Also, if you ran your CPU-o
Mark,
I've told about estimation of the energy of the ligands compounds
(small hormone-like compounds) embedded in the receptors binding
pocket.
In other words I want to simulate that ligands in water as well as in
the receptor complex and compare it's potential energy values in both
cases. From
Hi Mark,
I am not so sure regarding your point about a 2 fs timestep and
constraints = hbonds. Typical bond vibration between heavy atoms has
roughly a 20 fs period (see table I of the Feenstra et al. paper you
mentioned previously), so a timestep of 2 fs should be fine with
constraints = hbo
Dear Gmx Developer and Users,
*Is it possible for gromacs to use an 8-order or 9-oder cosine series for
dihedral angle computations?*
>From the menue, (Page 125, the table of Intramolecular Interactions
Definition)
there is one
--
interaction type directive # at. f. tp
pro
On Tue, Dec 4, 2012 at 11:30 AM, sebastian <
sebastian.wa...@physik.uni-freiburg.de> wrote:
> On 12/04/2012 05:09 PM, Mark Abraham wrote:
> > 2fs is normally considered too large a time step for stable integration
> > with only bonds to hydrogen constrained, so your observation of
> > non-reproduc
I can't know why you observe things working, in part because you haven't
said what's in this system :-) Pure inflexible water would be fine because
the constraints setting doesn't matter to water.
Moreover, whether integration issues cause things to crash can depend on
non-reproducible numerical e
Dear Gromacs users,
I have a question regarding position restraints on dihedral angles.
I would like to restrain the positions of phi and psi dihedral angles and on
top of that increase the potential barrier which needs to be over come in order
to go from one conformation to the next. (I.e. I w
On 12/04/2012 05:09 PM, Mark Abraham wrote:
2fs is normally considered too large a time step for stable integration
with only bonds to hydrogen constrained, so your observation of
non-reproducible LINCS warnings is not indicative of some other problem.
Sorry, but why is this whole setup run
2fs is normally considered too large a time step for stable integration
with only bonds to hydrogen constrained, so your observation of
non-reproducible LINCS warnings is not indicative of some other problem.
Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK this
works fine, b
Dear gromacs users
I would Like to Construct a assembly of cyclic Peptide Is there is Any On line
server or Tools Available ? Or any other Package Available
It would be helpful if somebody Assists me
Thanks In Advanve
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromac
On 11/23/2012 08:29 PM, Szilárd Páll wrote:
Hi,
On Fri, Nov 23, 2012 at 9:40 AM, sebastian<
sebastian.wa...@physik.uni-freiburg.de> wrote:
Dear GROMCS user,
I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on my
local desktop
Watch out, the dirty version suffix
On Tue, Dec 4, 2012 at 7:18 PM, Carsten Kutzner wrote:
>
> On Dec 4, 2012, at 2:45 PM, Chandan Choudhury wrote:
>
> > Hi Carsten,
> >
> > Thanks for the reply.
> >
> > If PME nodes for the g_tune is half of np, then if it exceeds the ppn of
> of
> > a node, how would g_tune perform. What I mean
On Dec 4, 2012, at 2:45 PM, Chandan Choudhury wrote:
> Hi Carsten,
>
> Thanks for the reply.
>
> If PME nodes for the g_tune is half of np, then if it exceeds the ppn of of
> a node, how would g_tune perform. What I mean if $NPROCS=36, the its half
> is 18 ppn, but 18 ppns are not present in a
Hi Carsten,
Thanks for the reply.
If PME nodes for the g_tune is half of np, then if it exceeds the ppn of of
a node, how would g_tune perform. What I mean if $NPROCS=36, the its half
is 18 ppn, but 18 ppns are not present in a single node (max. ppn = 12 per
node). How would g_tune function in s
Hi Chandan,
the number of separate PME nodes in Gromacs must be larger than two and
smaller or equal to half the number of MPI processes (=np). Thus, g_tune_pme
checks only up to npme = np/2 PME nodes.
Best,
Carsten
On Dec 4, 2012, at 1:54 PM, Chandan Choudhury wrote:
> Dear Carsten and Fl
Dear Carsten and Florian,
Thanks for you useful suggestions. It did work. I still have a doubt
regarding the execution :
export MPIRUN=`which mpirun`
export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5"
g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e
tune
On 12/4/12 3:10 AM, Tsjerk Wassenaar wrote:
Hi Jia,
You can use trjconv for custom fitting, and then feed the fitted trajectory
to g_rms, not using fitting there. Either that's using -nofit or -fit none.
The same can be done in one step by using an index file with g_rms and choosing
that g
On 12/3/12 11:55 PM, tarak karmakar wrote:
Thanks Justin
Yah! We can run steered MD or Umbrella Pulling ( sampling) for this
purpose. But one thing I am wondering that how to move the entire
complex. In my model there are no covalent bond ( bonding info)
between the metal and ligands. So how t
What components will that potential energy have?
Mark
On Mon, Dec 3, 2012 at 6:54 PM, James Starlight wrote:
> Dear Gromacs Users!
>
> I'm simulating different complexes of the receptors with different ligands.
>
> For each complex I want to determine potential energy (not the binding
> energy)
Hi Jia,
You can use trjconv for custom fitting, and then feed the fitted trajectory
to g_rms, not using fitting there. Either that's using -nofit or -fit none.
Cheers,
Tsjerk
On Tue, Dec 4, 2012 at 6:06 AM, Jia Xu wrote:
> Dear gromacs users,
> I have a trajectory of 500-atom system and
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