PDB file used :http://www.rcsb.org/pdb/explore.do?structureId=1cx2
Commands used: http://pastebin.com/raw.php?i=YYG5ad7A
Compressed folder containing all files (10.2 MB):
http://www.sendspace.com/file/rka8ei
So I want to simulate this complex. I am having problems with the .itp's
and do not know w
Hi Gromacs user community
a) I was wondering if it is possible to mix a common pair of PCs from
two simulations (say, PC1 from a bound simulation vs PC1 from unbound
simulation or for that matter wild vs mutant) as an reaction coordinates
to generate a comparative reduced free energy profile u
That is correct. Such a functionality wouldn't be that hard to
implement - but there are a long list of easy functionalities to be
implemented. You can submit a request to redmine.gromacs.org so that
the request is archived.
On Sat, Aug 3, 2013 at 6:12 PM, Dejun Lin wrote:
> So I take it that in
So I take it that in the position restraint case (not COM-pulling), where
the reference positions are determined by the starting structure instead of
a B-state topology, the reference positions won't be swapped ?
2013/8/3 Michael Shirts-2 [via GROMACS] <
ml-node+s5086n5010324...@n6.nabble.com>
>
Short answer is anything that has a B state parameter can be included
in in Hamiltonian exchange.
If it's pull code or explicit restraints, it's controlled by restraint lambda.
> I went through the manual and couldn't find any definite answers to the
> following questions.
>
> First, I wonder if
Hello,
I have a problem compiling Gromacs 4.6.3 on RHEL 6.4 x64 with permutations
of the following programs:
Intel 13.1.0
CUDA 5.5
OpenMPI 1.7.2
Cmake 2.8.11.2
FFTW 3.3.3 (or Intel MKL)
GNU 4.8.1
Basically, once the Intel compiler is introduced into the picture, NVCC
seems to fail:
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