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
--
gmx-us
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
./grompp_d
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
On Thu, Nov 1, 2012 at 8:45 PM, Justin Lemkul 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 increa
On 11/1/12 4:56 PM, Alex Marshall wrote:
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
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 i
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 Kelvin
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
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
too
Thanks a lot Sanku for your help.
On Thu, Nov 1, 2012 at 11:38 PM, Sanku M 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 along with the nati
hi Gmxers,
is the Hessian matrix unit in gmx is ps^(-2), or
J *mol^(-1) nm^(-2)?
thanks,
Yao
--
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search be
Thanks a lot Oliver for the useful information.
On Fri, Nov 2, 2012 at 12:26 AM, Oliver Beckstein 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 prese
>>> 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
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 most
Thanks for the information.
On Thu, Nov 1, 2012 at 10:56 PM, Justin Lemkul 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 contrib
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 behav
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.
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 wrote:
>
> 31 okt 2012 kl. 13.43 sk
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
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 whi
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...
6
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 b
As far as I know,
Glycam06 (AMBER) force field is not included in gromacs4.5.5.
If you want you can use amb2gmx.pl script that is available online or from
Erin Sorin's website at CSU @ Long Beach.
Remember that if you want to use GLYCAM06, its better to use AMBER ff99SB
or ff03 or the recent ff12
Hi,
On Nov 1, 2012, at 4:13 PM, Venkat Reddy 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 the optimized
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 ?
--
View this message in context:
http://grom
Hi,
Is carbohydrate forcefield in Charmm or Amber included in gromacs4.5.5
topology folders ?
Sanku
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before p
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
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
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 a
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
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
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 i
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 an
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
phos
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 d
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 yo
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
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 pull_in
38 matches
Mail list logo
