I have gone through the pull parameters in version 4.0 and 4.5 a bit more after
our previous discussion and I have found the following related to the value of
pull_init1.
pull_geometry = distance or direction generate the same distance at start with
grompp no matter what value is set to
On 2012-10-31 16:31, Yorquant Wang wrote:
Hi GMX-users,
Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently
provided Cholesterol parameters for Charmm FF. Does anyone have the
corresponding .itp file for cholesterol in GMX style?
Thanks for replying,
Yukun
there's a script
Hi David:
I have tested the script. The input are 1 charmm topology file,
2 corresponding charmm parameter file and 3 foldername. But there are a
lots of top_all***.rtf files and par_all***.prm files in
toppar_c36_aug12/toppar folder, I don't know which pair is the correct
pair. Could you
Dear Gromacs user,
This question is directed foremost on Berk Hess, but it may be
interesting also for other users.
Berk Hess evaluated the force between two ions separated by the LINCS
algorithm (Berk Hess et al Osmotic coefficients of atomistic NaCl force
fields).
My question is, how
Dear Colleagues,
I am currently carrying out MD simulations on models of archaeal
membranes. These membranes, contrary to those of bacteria or eukariota,
are made of unconventional lipids. In my case they contain a neutral
carbohydrate headgroup and the second one is a negatively charged
I'm trying to model a species for which the force field I'm using (OPLS-AA)
doesn't contain all the force constants needed for some of the groups
present. I've successfully defined several angle and dihedral force
constants using quantum mechanical simulations to generate potential energy
curves
31 okt 2012 kl. 13.43 skrev Justin Lemkul:
On 10/31/12 6:02 AM, bipin singh wrote:
Hello all,
Is there any way to calculate fraction of native contacts during the
simulation in gromacs. I searched the archives but didn't found any
significant clue.
At present, there is no way to do
On 2012-11-01 09:47, Yorquant Wang wrote:
Hi David:
I have tested the script. The input are 1 charmm topology file,
2 corresponding charmm parameter file and 3 foldername. But there are a
lots of top_all***.rtf files and par_all***.prm files in
toppar_c36_aug12/toppar folder, I don't know
On 11/1/12 9:19 AM, Ali Alizadeh wrote:
Dear All users
What difference is between two codes?
Read this: http://www.gromacs.org/Documentation/Terminology/Thermostats. I
don't know what LI and LG are (lithium and something else?) but likely the
latter approach is not correct.
-Justin
Hi,
I have two questions:
1-We can say The RMSD is commonly used as an indicator of convergence
of the structure towards an equilibrium state (Tsjerk W.). RMSD is
not sufficient to determine whether or not converge of
structure/system. Why?
2-Radius of gyration, RMSD, rmsd matrix are used as an
RMSD of what? Probably you mean RMSD from the starting (or crystal) structure.
First, consider that your profile
of RMSD vs. crystal structure levels off at 0.4 nm with increasing simulation
time. Consider how many possible
conformations are 0.4 nm RMSD away from the crystal structure. A stable
Dear all Gromacs users,
I have *two *questions:
1) I have been doing my simulation on a computer having 24
processors. I issued *g_tune_pme -s *.tpr -launch *command to
directly launch my *mdrun *with the optimized settings. At the end of
optimization, g_tune_pme has given -npme as
Hi,
Is carbohydrate forcefield in Charmm or Amber included in gromacs4.5.5
topology folders ?
Sanku
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Dear all,
My system consists of Two walls of carbon atoms but I am not able to view
the carbon atom walls in VMD.
Also my topology file have no information about wall atoms.
So is it possible to see them somehow or my system has no walls indeed ?
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Hi,
On Nov 1, 2012, at 4:13 PM, Venkat Reddy venkat...@gmail.com wrote:
Dear all Gromacs users,
I have *two *questions:
1) I have been doing my simulation on a computer having 24
processors. I issued *g_tune_pme -s *.tpr -launch *command to
directly launch my *mdrun *with
I gave My cmd Prompt output for satisfactorily shrunken
system as follows
Reading.
Scaling lipids
There are 127 lipids...
with 50 atoms per lipid..
Determining upper and lower leaflet...
64 lipids in the upper...
63 lipids in the lower leaflet
Centering protein
Writing scaled
On 11/1/12 12:48 PM, vidhya sankar wrote:
I gave My cmd Prompt output for satisfactorily shrunken
system as follows
What was your command that produced this output?
Reading.
Scaling lipids
There are 127 lipids...
with 50 atoms per lipid..
Determining upper and lower leaflet...
hello:
I am running a 40ns REMD with GBSA solvent NPT simulations. It is
exchange for 16 different temperature with exchange step 300.
mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s
remd_.tpr -multi 16 -replex 300
I found that it will require 1 months to be finished
On 11/1/12 12:55 PM, Albert wrote:
hello:
I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for
16 different temperature with exchange step 300.
Based on your .mdp file, you're not doing NPT (pcoupl = no).
mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb
Thanks for your response. Hope to see this feature in upcoming GROMACS
release. Before that, could it be possible to get the modified code in the
user contribution section, it may be useful for many GROMACS users.
On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
31
On 11/1/12 1:23 PM, bipin singh wrote:
Thanks for your response. Hope to see this feature in upcoming GROMACS
release. Before that, could it be possible to get the modified code in the
user contribution section, it may be useful for many GROMACS users.
If someone writes the code, certainly.
On 11/1/12 12:25 PM, Ali Alizadeh wrote:
Dear Justin
These attachments are my rdf,g(r) profiles,
http://tb18.trainbit.com/d/8692999884.jpg
http://tb18.trainbit.com/d/6692999884.jpg
http://tb18.trainbit.com/d/9692999884.jpg
You've got an inhomogeneous system; you can't expect it to
Thanks for the information.
On Thu, Nov 1, 2012 at 10:56 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/1/12 1:23 PM, bipin singh wrote:
Thanks for your response. Hope to see this feature in upcoming GROMACS
release. Before that, could it be possible to get the modified code in the
user
Bipin,
There might be a workaround. You might want to check out Plumed plugin in
latest versions of VMD for calculating fractions of native contact. You can
load the gromacs trajectory along with the native .gro file in VMD and use
Plumed plugin inbuilt in VMD . You need to install plumed
Is there any way to calculate fraction of native contacts during the
simulation in gromacs. I searched the archives but didn't found any
significant clue.
At present, there is no way to do this. Likely one could modify the
g_mindist code to do this - it would be a very nice feature.
Thanks a lot Oliver for the useful information.
On Fri, Nov 2, 2012 at 12:26 AM, Oliver Beckstein obeck...@asu.edu wrote:
Is there any way to calculate fraction of native contacts during the
simulation in gromacs. I searched the archives but didn't found any
significant clue.
At
hi Gmxers,
is the Hessian matrix unit in gmx is ps^(-2), or
J *mol^(-1) nm^(-2)?
thanks,
Yao
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Thanks a lot Sanku for your help.
On Thu, Nov 1, 2012 at 11:38 PM, Sanku M msank...@yahoo.com wrote:
Bipin,
There might be a workaround. You might want to check out Plumed plugin
in latest versions of VMD for calculating fractions of native contact. You
can load the gromacs trajectory
Hey :)
If I say something is commonly used, I don't mean that the usage is correct
:p Chris' answer is quite good though, and I can't add much more, except
maybe that the RMSD, being a distance, isn't a good indicator of
convergence, when it reaches the point of saying 'far away'. There's just
Dear Christopher,
Firstly thanks for your reply. RMSD is a measure related with whether or
not converge of particles in the structures versus the starting structure.
In other word, it is the difference (average distance) between the
positions of particles in two structures. Conformational changes
On 11/1/12 4:36 PM, Steven Neumann wrote:
Dear Gmx Users,
I have system with protein in water. I equlibrated it in at 300 K and
1 bar for 5 ns with position restrained of protein heavy atoms. I run
script at NP and increasing temperature from 300K to 600 K with
changing temperature of 1
I've created a position restraint file for the specific waters that I need
to immobilize, but I'm having a hard time getting grompp to apply it
successfully. No matter where I put #include posre.itp in my topology
file grompp returns fatal errors about the atomic indices being out of
bounds. Is it
On Thu, Nov 1, 2012 at 8:45 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/1/12 4:36 PM, Steven Neumann wrote:
Dear Gmx Users,
I have system with protein in water. I equlibrated it in at 300 K and
1 bar for 5 ns with position restrained of protein heavy atoms. I run
script at NP and
On 11/1/12 5:49 PM, Ali Alizadeh wrote:
Dear All usres
I have a system that contains water , methane and propane in 240 k and 300
bar,
My simulation box is rectangular .
Water film is in middle of my box. Methane and propane is around it.
I have a problem, my methane and propane molecules
As uou Told me in the Previous Mail I have Given My sereis of Commands With
Real file Names
./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc
./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c
./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3 -box 6 6 6
Dear all,
I am running a system with sol 40646 atom and ion, NA 629 CL 634.
At the time of nvt and npt should i have to make different *tc_grps* for
ion and sol or should be make one group
Nonprotein ( these include sol + ion)..these is default.
With Best wishes and regards,
Rama david
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