I couldn't get you. Does it means that for pre-positioning say 40 molecules
of Arginine do I need to create 40 pdb of different coordinate then combine
it with pdb of protein and then use pdb2gmx. I want to use different number
of free positively charged Arginine molecule in simulation box along
shahid nayeem wrote:
I couldn't get you. Does it means that for pre-positioning say 40
molecules of Arginine do I need to create 40 pdb of different coordinate
then combine it with pdb of protein and then use pdb2gmx. I want to use
different number of free positively charged Arginine
I have asked you before to keep all discussion on the gmx-users list. Please do
so. It exists so that users can ask these types of questions and that others in
the community can learn and contribute.
I don't understand why you're running pdb2gmx on a system that already has a
topology and
Dear all,
searching for the mentioned error message I found a bug report for
mdrun. It seemed to be fixed, but in my setup it appears again and I am
not sure if I could do something about it.
I did not attach the tpr file since it is bounced by the mailing list
and I'd like to get at least
I tried with single Arginine molecule pdb.
pdb2gmx -f arg.pdb -o arg.gro -p arg.top
genconf -f arg.gro -nbox 2 2 2 -o seq.gro
genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro
-box 1.8 1.8 1.8
command runs but it does not add protein.pdb to the box
shahid nayeem
On Fri, Aug
shahid nayeem wrote:
I tried with single Arginine molecule pdb.
pdb2gmx -f arg.pdb -o arg.gro -p arg.top
genconf -f arg.gro -nbox 2 2 2 -o seq.gro
genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro
-box 1.8 1.8 1.8
command runs but it does not add protein.pdb to the box
Hello,
Please let me know from where can I get the full description of g_sham
module, as the manual does not
provide full description of the options for g_sham in gromacs.
for e.g I want to know the description about the following options in g_sham:
-map
-ls3
-mdata
--
Dear users,
I have done some 16 simulations of a protein with mutations,
by keeping the distance between protein atom and the simulation
box to be 1.0nm (i.e, -d option in editconf) but only in one of the
simulation I found violation of minimum image distance. So Should
I increase the box size
Kavyashree M wrote:
Dear users,
I have done some 16 simulations of a protein with mutations,
by keeping the distance between protein atom and the simulation
box to be 1.0nm (i.e, -d option in editconf) but only in one of the
simulation I found violation of minimum image distance. So Should
I
Sir,
Yes I was the one who posted that. I understand that, I had used
dodecahedron and the problem here is- since i need to compare
these simulations is it ok if i increase the size of the box for only this
system (which is problematic) and redo the simulation or do i need to
do for all 16. I
On 12/08/2011 11:09 PM, Kavyashree M wrote:
Sir,
Yes I was the one who posted that. I understand that, I had used
dodecahedron and the problem here is- since i need to compare
these simulations is it ok if i increase the size of the box for only this
system (which is problematic) and redo the
On 12/08/2011 9:55 PM, Sebastian Breuers wrote:
Dear all,
searching for the mentioned error message I found a bug report for
mdrun. It seemed to be fixed, but in my setup it appears again and I
am not sure if I could do something about it.
I did not attach the tpr file since it is bounced
On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers
breue...@uni-koeln.de wrote:
Dear all,
searching for the mentioned error message I found a bug report for mdrun. It
seemed to be fixed, but in my setup it appears again and I am not sure if I
could do something about it.
I did not attach
Dear GMX users,
I am using GMX4.5.4 to simulate SWM4-NDP polarizable water model, it is
OK. But when I use the ions polarizable model which is in conjuction with
SWM4-NDP model, the RMS force is very large:
step 16: EM did not converge in 20 iterations, RMS force 7.950
step 17: EM did not
Hey,
thank you both for the response. I at least could restart the system.
And it is running beyond the crashing point. Keep the fingers crossed. :)
Kind regards
Sebastian
Am 12.08.2011 15:41, schrieb lina:
On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers
breue...@uni-koeln.de wrote:
hello
Just to share information. My parallel MD run also crash (very rarely) but I
can always bypass the crash point using cpt files.
dawei
On Fri, Aug 12, 2011 at 10:02 AM, Sebastian Breuers
breue...@uni-koeln.dewrote:
Hey,
thank you both for the response. I at least could restart the
Hi all,
I have thought of three experimental values to validate the parameters I
assigned for a oligosaccharide, namely, free enthalpy of solvation, nOe
effect, and some J3-couplings.
For free enthalpy of solvation, I wondered why delta G was used to indicate
enthalpy? Would what be measured is
I am quite interested in seeing this functional in GROMACS. You appear
to have been more successful than me so far. However, I believe from
reading the papers that the Drude particle (OD_swm4ndp) should have a
mass of 0.40 while the oxygen should have a mass of 15.59994 (the true O
mass is
Hi,
I was using gromacs 4.0.7 to calculate the scattering intensity of polymer
solvated in a solvent. But, I found a discrepancy in the normalization of the
calculation when considering only a subset
of the entire system ( e.g . only solute from the entire solution) :
This is what I found:
Dear gromacs users,
I am using gromacs 4.0.7 or higher and I would like to
ask you two simple questions.
For a certain purpose, I use gromacs (grompp or mdrun)
many times, and the same information appear on the
screen, which might make the computational process slow.
How can I suppress
Hiroshi Fujisaki wrote:
Dear gromacs users,
I am using gromacs 4.0.7 or higher and I would like to
ask you two simple questions.
For a certain purpose, I use gromacs (grompp or mdrun)
many times, and the same information appear on the
screen, which might make the computational process
Dear Justin,
Thanks for your prompt reply and help.
I understood about the first item, but even if I type
export GMX_MAXBACKUP=0 (bash)
it does not seem to work. What is the recommended
procedure? Is there any problem with revision?
I appreciate your help.
Best wishes,
Hiroshi Fujisaki
It is possible that the terminal that used to run gromacs does not have
GMX_MAXBACKUP set up. if you use some queue software, put export
GMX_MAXBACKUP=0 in the submitting script or even put it into your .bashrc
file.
On Fri, Aug 12, 2011 at 1:53 PM, Hiroshi Fujisaki fujis...@nms.ac.jpwrote:
Dear All,
When I try to grompp to generate .tpr file for mdrun from
topology generated by prodrg I am getting the following error.
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'PRODRG'
Ravi Kumar Venkatraman wrote:
Dear All,
When I try to grompp to generate .tpr file for mdrun from
topology generated by prodrg I am getting the following error.
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'PRODRG'
Dear all,
Please can anybody send, step by step mdrun for small organic
molecules in gromacs.
Dear All,
When I try to grompp to generate .tpr file for mdrun from
topology generated by prodrg I am getting the following error.
Generated 279 of the 1225 non-bonded
I could not find out what is wrong I tried add to add #include ions.itp
and #ifdef but it is not successful.
Fatal error:
No such moleculetype SOL
Please help me. I got stuck with this. Please.
--
gmx-users mailing listgmx-users@gromacs.org
Ravi Kumar Venkatraman wrote:
I could not find out what is wrong I tried add to add #include
ions.itp and #ifdef but it is not successful.
SOL is water, not ions. #include an appropriate water model.
-Justin
Fatal error:
No such moleculetype SOL
Please help me. I got stuck with this.
Hi Ravi,
SOL does not sound like an ion to me. You probably want to include the
topology for a water model, like spc.itp
It sounds like you're trying things without knowing what, the way you
mention #include and #ifdef. Did you try the tutorial material already?
Cheers,
Tsjerk
On Aug 12, 2011
Dear gmx-users,
I am trying to learn viscosity calculations using non-equilibrium
method in Gromacs 4.5.4. I have gone through Hess paper and several
posts on viscosity calculation.
I have setup a system of pure water (32000 molecules) and run till 10 ns
using NPT and setting
cos-acceleration=0.1
Hi all,
I am trying to do a calculation on an artificial line charge in vacuum. The
line charge has 267 atoms and each atom has a 1e charge. The atoms are
bonded by a bond term and an angle term. I defined the required itp files
and top file. When i issue
grompp_jpt -v -c parallel.gro -p
Amit Choubey wrote:
Hi all,
I am trying to do a calculation on an artificial line charge in vacuum.
The line charge has 267 atoms and each atom has a 1e charge. The atoms
are bonded by a bond term and an angle term. I defined the required itp
If you're trying to keep the atoms in a line,
On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi all,
I am trying to do a calculation on an artificial line charge in vacuum.
The line charge has 267 atoms and each atom has a 1e charge. The atoms are
bonded by a bond term and an angle term.
Amit Choubey wrote:
On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi all,
I am trying to do a calculation on an artificial line charge in
vacuum. The line charge has 267 atoms and each
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