Dear All,
I am planning to perform a QM/MM calculation of my protein system. Can
anybody suggest me whether gromacs-4.5.5 can be patched with any latest
version of CPMD? If not, then please suggest me some combination of the
gromacs-cpmd versions.
I came across this tutorial, but there, both
Am 8/12/13 5:26 AM, schrieb Kieu Thu Nguyen:
Dear users,
I want to use g_msd to measure diffusion coefficients of lipid bilayer. But
i do not know how to choose the reference atom per lipid for an any type of
lipid, such as POPC, DOPC,...
Where i can get these references ?
One
This is
Sent from my iPhone
On Aug 14, 2013, at 1:40, Albert mailmd2...@gmail.com wrote:
Does anybody have any idea what's the problem?
I use the tutorial example and I don't know why it doesn't work.
THX
On 08/13/2013 07:19 PM, Albert wrote:
Dear:
I am trying to run plumed with
This is a plumed error, not a gromacs error. Gromacs never handles those
keywords.
Sent from my iPhone
On Aug 14, 2013, at 1:40, Albert mailmd2...@gmail.com wrote:
Does anybody have any idea what's the problem?
I use the tutorial example and I don't know why it doesn't work.
THX
On 08/14/2013 12:26 PM, Michael Shirts wrote:
This is a plumed error, not a gromacs error. Gromacs never handles those
keywords.
Sent from my iPhone
IC
THX, it works now. I found some strange characters in the plumed.dat
file. After delete them, it work now
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Hello:
I am producing MD production with command:
mpirun -np 24 mdrun_mpi -plumed plumed.dat -s md.tpr -v -g md.log -x
md.xtc -o md.trr -e md.edr
I notice that it generate two additional files:
HILLS COLVAR
the output in this two files are very frequent such as:
#! FIELDS time cv1 cv2
On 8/13/13 10:26 PM, Pedro Lacerda wrote:
Hi all,
Many questions about how to choose a force field are addressed to this
list, sorry if this one was already answered.
Some argue that proteins are better modeled with ff99sb-ildn or charmm22*
because occur great agreement between NMR
On 8/14/13 9:43 AM, Albert wrote:
Hello:
I am producing MD production with command:
mpirun -np 24 mdrun_mpi -plumed plumed.dat -s md.tpr -v -g md.log -x md.xtc -o
md.trr -e md.edr
I notice that it generate two additional files:
HILLS COLVAR
the output in this two files are very frequent
Hi gmx-users and gmx-developers,
There are a number of features of GROMACS that we plan to drop for 5.0
(scheduled for early 2014). We don’t like doing this, but if things
are broken or cause developers pain, then they will go unless there is
manpower to support them. We’d like to keep you
Hello all,
Does anyone know if there is a working version of charmm36 proteins
forcefield converted for gromacs?
Thank you.
-Dina
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* Please search the archive at
Dear users,
I am attempting to determine the free energy of self solvation of several
small molecules.
Starting with an equilibrated box of pure fluid (for example, ethanol -
which I am calling thr) I am renaming all of the molecules except for the
first in the .gro file SOL, then updating the
I found the error, I had B states defined for my solvent molecules in the
topology file.
On Wed, Aug 14, 2013 at 2:47 PM, Brittany Zimmerman bsz...@virginia.eduwrote:
Dear users,
I am attempting to determine the free energy of self solvation of several
small molecules.
Starting with an
I am interested in Generalized Born. My coding skills are limited, but I
would like to help to whatever extent I can.
I am also interested in helping towards revamping the tutorials if the need
should arise.
On Wed, Aug 14, 2013 at 8:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Hi
From my inspection of the force field files included in gromacs-4.6.1, when you
use the charmm ff and the charmm tip3p (tips3p.itp) you get the hydrogen type
HT,
which does have LJ on the hydrogen atoms, whereas you only get the hydrogen
type HWT3 when you use the non-charmm tip3p (tip3p.itp).
What is the charmm36 protein force field? (can you provide a reference to what
you are referring to).
As far as I know, there is no such thing as charmm36 proteins. There are
charmm27+cmap proteins
(implemented in gromacs already) and charmm36 lipids (implemented in gromacs
already).
--
On 8/14/13 6:22 PM, Christopher Neale wrote:
What is the charmm36 protein force field? (can you provide a reference to what
you are referring to).
As far as I know, there is no such thing as charmm36 proteins. There are
charmm27+cmap proteins
(implemented in gromacs already) and charmm36
Hi everybody.
I wonder how the sign convention of GROMACS (or better g_energy ) is: Is U(state_i):= E_tot (state_i)_t correct or do i have to choose the other sign U(state_i)= -1.0* E_tot (state_i)_t ? (_t denotes the time average)
I need the correct sign for further calculations since i need
On 8/14/13 6:42 PM, gg jj wrote:
Hi everybody.
I wonder how the sign convention of GROMACS (or better g_energy ) is: Is
U(state_i):= E_tot (state_i)_t correct or do i have to choose the other sign
U(state_i)= -1.0* E_tot (state_i)_t ? (_t denotes the time average)
I need the correct sign for
TIP3P and TIPS3P (which I found later is the CHARMM TIP3P) produce slightly
different water bulk density:
0.96 vs. 1.01 when using CHARMM ff set, but TIPS3P is almost two times
slower than original TIP3P. For the benefit of TIPS3P, I think it heavily
depends on applications.
Weilong
Christopher
Thanks Justin. I will just modify the existing charmm files for gromacs to
make the charmm36 version. I just wanted to see if anyone had already done
this, so as not to redo something that's already been done.
-D
On Wed, Aug 14, 2013 at 6:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On
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