Dear Carlos,
You get a double contribution from MainChain and SideChain in this way, don't
you?
Kind regards,
Erik
On 19 Nov 2014, at 03:00, Carlos Navarro Retamal cnava...@utalca.cl wrote:
Dear gromacs users,
I’m studying the hydrogen bond interaction between a protein and different
Justin,
I have used the paramchem software as suggested by you. I
submitted my pdb file and CGENFF gave a .str file as output. Now could you
please tell me how to proceed to obtain the .itp file? Also is it sensible
to use SWISSPARAM since it gives .itp from .mol2 directly? Once I have
Thank you Justin,unfortunatly i tried to use your solution, but there are some
problems with free energy use in REST. The first is that free energy
interpolate from state A to state B, but can't manage to interpolate proper
multiple dihedrals, so i don't know how to treat dihedrals with this
Hi Priya,
You can use genconf with the option -box to replicate your box (in this
case your membrane) as many times as you want in the x,y and z directions.
Keep in mind that -box only deals with integers (number of boxes), so
something like -box 1.5 2.5 1 will be equivalent to -box 2 3 1. If the
On 11/19/14 6:16 AM, Catarina A. Carvalheda dos Santos wrote:
Priya,
Did you perform at least one energy minimization step before that? Because
you should, one or several, to remove unfavorable interactions.
...and even more importantly: were the DPPC whole (or at least made whole) prior
I used dppc.128 (128 DPPC lipids and 3655 water molecules) for replicating
.
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On Wed, Nov 19, 2014 at 10:38 AM, Carlo Martinotti
carlo.martino...@studenti.unimi.it wrote:
Thank you Justin,unfortunatly i tried to use your solution, but there are
some problems with free energy use in REST. The first is that free energy
interpolate from state A to state B, but can't
On 11/19/14 4:33 AM, soumadwip ghosh wrote:
Justin,
I have used the paramchem software as suggested by you. I
submitted my pdb file and CGENFF gave a .str file as output. Now could you
please tell me how to proceed to obtain the .itp file? Also is it sensible
Use our converter;
Dear Justin,
Thanks for ypour reply.
My runs are getting failed at multiple lambda values, say 4 out of 21. For
some cases, these runs go fine when I change pcouple to berendsen. Is it
acceptable to use berendsen instead of PR for such simulations.
I guess I need to do more equilibration on my
Hi,
That work treats the constraint algorithm as a black box that accurately
computes the Lagrangian multipliers; the abstract is worded as SHAKE-type
constraints etc. So the properties of any other method that computes the
multipliers satisfactorily (e.g. LINCS) follow immediately.
Mark
On
FYI: Last time I tried the HREX using the PLUMD2 patch (this was about
a year ago), I did not need to did any kind of temperature tricks at
all!
--
Szilárd
On Tue, Nov 18, 2014 at 4:44 PM, Carlo Martinotti
carlo.martino...@studenti.unimi.it wrote:
I'm trying to run a hamiltonian REMD simulation
On Wed, Nov 19, 2014 at 2:50 PM, vivek sharma viveksharma.i...@gmail.com
wrote:
Dear Justin,
Thanks for ypour reply.
My runs are getting failed at multiple lambda values, say 4 out of 21. For
some cases, these runs go fine when I change pcouple to berendsen. Is it
acceptable to use berendsen
Hello all,
Do we need to create a box using editconf before using grompp to carry
out energy minimization between shrinking steps.???
Thanks,
Padmani
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On Wed, Nov 19, 2014 at 7:25 PM, Soren Wacker swac...@ucalgary.ca wrote:
Hi,
I have trouble to install gromacs 5.0.2 in double precision with shared
fftw libraries. During the cmake process I get:
Could not find fftw3 library named libfftw3, please specify its location
in CMAKE_PREFIX_PATH
Hi,
You did choose to get involved with details, rather than using
CMAKE_PREFIX_PATH... :-)
Mark
On Wed, Nov 19, 2014 at 11:05 PM, Soren Wacker swac...@ucalgary.ca wrote:
So, when I compile in double precision it must be
-DFFTW_INCLUDE_DIR=~/Programme/fftw3/double/include \
when it is
On 19 Nov 2014, at 20:03, Soren Wacker swac...@ucalgary.ca wrote:
Hi Carsten!
Like this??
-DCMAKE_PREFIX_PATH=“/global/software/boost/gcc:~/Programme/fftw3/double/ \
The above line should be right, I assume.
Carsten
or like this?
-DCMAKE_PREFIX_PATH=/global/software/boost/gcc \
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