Thank you David, I got it now. For future reference of the list, my initial
confusion was because I had misinterpretated that ADH is an alternate
*implementation* of DHA. But really, ADH is an independent geometric
*definition*.
-Rob
> Date: Fri, 6 Feb 2009 22:32:48 +0100
> From: sp...@xray.b
rob yang wrote:
At the risk of exposing my density in triangle geometry here, why does
180-DHA = ADH?
H
/ \
D - A
This shows it... I confused it even further. The angle we have been
using since 3.2 is HDA. If 0, it is perfect, if more than 30 (-acut
option) it is not counted
He, Yang wrote:
Hi, I just got this CG DNA model from a paper as well as the required
parameters . What you think I should deal with the interactions about hydrogen
bonding ? I have defined all the atoms' charge as 0 but still the repelling
happened.
The interactions holding DNA together
Hi, I just got this CG DNA model from a paper as well as the required
parameters . What you think I should deal with the interactions about hydrogen
bonding ? I have defined all the atoms' charge as 0 but still the repelling
happened.
Yang
From: gmx-user
At the risk of exposing my density in triangle geometry here, why does 180-DHA
= ADH?
H
/ \
D - A
Thank you.
-Rob
> Obviously the DHA angle in a linear Hbond is
> 180, so it should either be 180-DHA or ADH. The ADH angle is what's
> implemented in gromacs > 3.2.1, however in
Casey,Richard wrote:
Hi,
We've been able to merge a compound in a membrane (popc128) with
genbox -cp compound.pdb -cs popc128a.pdb -box 8 8 8 -o compound_in_popc128.pdb
-p compound.top
however it places the compound near the edge of the membrane. We would like to place the compound at o
Hi,
We've been able to merge a compound in a membrane (popc128) with
genbox -cp compound.pdb -cs popc128a.pdb -box 8 8 8 -o compound_in_popc128.pdb
-p compound.top
however it places the compound near the edge of the membrane. We would like to
place the compound at other (various) locations
osmair oliveira wrote:
Hi Justin,
Ok, now, I try to install without mpicc, but I have the error:
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -o ffscan ffscan.o glaasje.o gctio.o init_sh.o
ionize.o md.o genalg.o do_gct.o relax_sh.o repl_ex.o xutils.o
On Feb 6, 2009, at 1:55 PM, David van der Spoel wrote:
Joshua Ballanco wrote:
Hello all,
Apologies if this is obvious, but I've been reading through the
manual and various Google searches and come up empty-handed. My
question is if it is possible to construct an infinite polymer
chain in
Joshua Ballanco wrote:
Hello all,
Apologies if this is obvious, but I've been reading through the manual
and various Google searches and come up empty-handed. My question is if
it is possible to construct an infinite polymer chain in Gromacs? That
is, I'd like to setup a cell with PBC, but ha
Hi Justin,
Ok, now, I try to install without mpicc, but I have the error:
cc
-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -o ffscan ffscan.o glaasje.o gctio.o init_sh.o
ionize.o md.o genalg.o do_gct.o relax_sh.o repl_ex.o xutils.o
compute_io.o -L/home/osmair
Joshua Ballanco wrote:
Hello all,
Apologies if this is obvious, but I've been reading through the manual
and various Google searches and come up empty-handed. My question is if
it is possible to construct an infinite polymer chain in Gromacs? That
is, I'd like to setup a cell with PBC, but
osmair oliveira wrote:
mpicc: No such file or directory
It appears that you either don't have mpicc installed, or it is not within your
PATH.
-Justin
--
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksb
Hi,
VAR should be an environment variable that is set by your MPI implementation.
Try:
mpirun -np 2 env
For OpenMPI I use:
OMPI_MCA_universe
Berk
Date: Fri, 6 Feb 2009 16:38:57 +
Subject: Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2
From: jmda...@itqb.unl.pt
To: gmx-use
Hi,
I am trying to install gromacs333 with mopac. I use the command:
./configure --enable-mpi --with-qmmm-mopac CPPFLAGS=-DUSE_MOPAC
LDFLAGS=-L/home/osmair/qmmm/ -LD_LIBRARY_PATH=-lmopac
However I found the following error when I run make:
mpicc -O3 -fomit-frame-pointer -finline-functions -
Hi,
sorry for the late answer. But there is a completely new g_wham in the
most recent gmx version 4.xx. With this one, the error
"This does not appear to be a valid pdo file"
does not occur any more. And the new g_wham provides a lot of new
featues, too.
Best,
Jochen
anirban polley wrote:
>
Hello all,
Apologies if this is obvious, but I've been reading through the manual
and various Google searches and come up empty-handed. My question is
if it is possible to construct an infinite polymer chain in Gromacs?
That is, I'd like to setup a cell with PBC, but have one end of my
mo
On Fri, Feb 6, 2009 at 4:12 PM, Berk Hess wrote:
> Hi,
>
> I always compile Gromacs with --enable_mpi --enable-mpi-environment=...
> such that you can run a serial mdrun without using mpirun.
>
Interesting. So what does that "..." (or VAR in the help of configure)
means? I'm sorry, but I can't
Hi,
I always compile Gromacs with --enable_mpi --enable-mpi-environment=...
such that you can run a serial mdrun without using mpirun.
Berk
Date: Fri, 6 Feb 2009 15:22:54 +
Subject: Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2
From: jmda...@itqb.unl.pt
To: gmx-users@grom
On Mon, Jan 19, 2009 at 6:09 PM, Berk Hess wrote:
> Hi,
>
> When running in parallel on a cluster through a queuing system
> one usually does not (or can not) see or check the nice level
> of the mdrun processes. But the nice level can have a significant
> impact on performance, especially when
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