Hi all,
I'm trying to extract the nonbonded interaction parameters for a whole system
from the text dump generated by gmxdump (-s topol.tpr). I get it the relevant
section is something like this:
atnr=7
ntypes=50
functype[0]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
functype[1]=LJ_SR, c6=
I tried to solvate an assembly of amyliod peptides (16 peptide), using editconf
and genbox respectively as follow,
editconf -f rotated.gro -box 76 6 6 -center 0 0 0 -o rotated-box
then,
genbox -cs ffamber_tip3p.gro -cp rotated-box -p fragment -o sol
when, I tried to visualize the protein using
On 13/05/11, Ignacio Fernández Galván wrote:
> Hi all,
>
>
> I'm trying to extract the nonbonded interaction parameters for a whole system
> from the text dump generated by gmxdump (-s topol.tpr). I get it the relevant
> section is something like this:
>
> atnr=7
> ntypes=50
> functype[0]=
On 13/05/11, Asmaa Elsheshiny wrote:
>
> I tried to solvate an assembly of amyliod peptides (16 peptide), using
> editconf and genbox respectively as follow,
> editconf -f rotated.gro -box 76 6 6 -center 0 0 0 -o rotated-box
>
Nothing here does any rotation.
>
> then,
> genbox -cs ffa
vidhya sankar wrote:
Dear Justin thank you for your previous mail When i do Steered MD ,
During final MD i got the following message in command prompt is it
critical error OR may i ignore this message
What will i do to avoid this error? I am seeing negative pull rate
Pull reference distanc
Hi,
> I tried to solvate an assembly of amyliod peptides (16 peptide), using
> editconf and genbox respectively as follow,
> editconf -f rotated.gro -box 76 6 6 -center 0 0 0 -o rotated-box
>
> Nothing here does any rotation.
Well, it seems something that was rotated goes in... that seems fine
Dear gmx-users,
I'm simulating a homodimeric protein obtained by homology modelling. In the
.pdb file, I have 2 chain identifiers (A and B). I used Gromacs 4.0.7 to
prepare the .gro files for simulation (up to nvt); then I was forced to
switch to Gromacs 4.5.4 on another machine to continue with np
Anna Marabotti wrote:
Dear gmx-users,
I'm simulating a homodimeric protein obtained by homology modelling. In
the .pdb file, I have 2 chain identifiers (A and B). I used Gromacs
4.0.7 to prepare the .gro files for simulation (up to nvt); then I was
forced to switch to Gromacs 4.5.4 on anothe
On 13/05/11, Anna Marabotti wrote:
>
>
>
>
>
>
>
>
>
>
> Dear
> gmx-users,
>
> I'm simulating a
> homodimeric protein obtained by homology modelling. In the .pdb file, I have
> 2
> chain identifiers (A and B). I used Gromacs 4.0.7 to prepare the .gro files
> for
> simulation (u
Dear Justin,
thank you very much for infos. I was aware that in Gromacs 4.5.4 pdb2gmx
does not renumber the PDF file anymore; what seems strange to me is that
Gromacs 4.5.4 "backnumbered" also a .gro file that was already renumbered by
4.0.7, without using pdb2gmx (I only took the nvt.gro and nvt.t
Anna Marabotti wrote:
Dear Justin,
thank you very much for infos. I was aware that in Gromacs 4.5.4 pdb2gmx
does not renumber the PDF file anymore; what seems strange to me is that
Gromacs 4.5.4 "backnumbered" also a .gro file that was already renumbered by
4.0.7, without using pdb2gmx (I only
Hello,
I am using NPT simulation for water - spce model (opls-aa force field).
I have the reference pressure set at ref_p = 1.0 bar.
I checked the average pressure using g_energy and it is 2.81972 bar.
Why there increase in pressure?
For NVT simulatin I get the value around average pressure 71
Nilesh Dhumal wrote:
Hello,
I am using NPT simulation for water - spce model (opls-aa force field).
I have the reference pressure set at ref_p = 1.0 bar.
I checked the average pressure using g_energy and it is 2.81972 bar.
Why there increase in pressure?
Probably the system is not yet equ
ure".
In any case, you need to identify where it first arose in your workflow in
order to work out why it happened and what to do about it.
Mark
>
>
>
>
>
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any case, you need to identify where it first arose in your workflow in
order to work out why it happened and what to do about it.
Mark
>
>
>
>
>
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (54
Dear Justin
Thanks for your reply. Generally I conduct the simulation following the
tutorial on your website. The system contains an integrin alpha2b/beta3
transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer and
solvated in water. The initial membrane-protein system is built
li lv wrote:
Dear Justin
Thanks for your reply. Generally I conduct the simulation following the
tutorial on your website. The system contains an integrin alpha2b/beta3
transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer
and solvated in water. The initial membrane-pro
Hello.
I am writing to ask if current GROMACS-GPU supports CMAP dihedrals in
CHARMM.
We are trying to run GROMACS on GPU. It is mentioned on GROMACS website
(http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu)
that CMAP dihedrals in CHARMM are not support. However,
Hello Justin,
I used 0.1fs timestep and I could get dielectric constant around 56 which
looks ok. To get the dielectric constant around ~75, should I reduce the
timestep around 0.05fs.
I used temperature 298k for my simulation and average tmep. I got is
297.83 K. I am doing NPT and used 1.0 bar a
Nilesh Dhumal wrote:
Hello Justin,
I used 0.1fs timestep and I could get dielectric constant around 56 which
looks ok. To get the dielectric constant around ~75, should I reduce the
timestep around 0.05fs.
I have no idea. Try it.
I used temperature 298k for my simulation and average tmep
Hello,
I have a quick question about g_energy output. Can anyone descrive how the
statistical info below are calculated?
In literature I see for instance electrostatics is reported as: XXX + / -
Y. Where Y is deviation or something like that. Which of the RMSD or
Tot-Drift is giving Y ?
g_energy
Juliette N. wrote:
Hello,
I have a quick question about g_energy output. Can anyone descrive how
the statistical info below are calculated?
In literature I see for instance electrostatics is reported as: XXX + /
- Y. Where Y is deviation or something like that. Which of the RMSD or
Tot-
Greetings,
I have been running simulations of 254 SPC/E water molecules using the OPLS
force field. As Nilesh mentioned earlier today, I am using the NPT
ensemble. I am setting the reference pressure at 1 bar, but when I do a
sequence of minimization, equilibration, and dynamics steps, and then
Andrew DeYoung wrote:
Greetings,
I have been running simulations of 254 SPC/E water molecules using the OPLS
force field. As Nilesh mentioned earlier today, I am using the NPT
ensemble. I am setting the reference pressure at 1 bar, but when I do a
sequence of minimization, equilibration, and
On 14/05/2011 11:02 AM, Andrew DeYoung wrote:
Greetings,
I have been running simulations of 254 SPC/E water molecules using the OPLS
Bear in mind that this is a tiny system, and that temperature and
pressure are macroscopic quantities. Reliable measurements of them need
long times and lots o
Which QM method in Gromacs are you using?
On Tue, May 10, 2011 at 5:41 PM, Yao Yao wrote:
> Hi gmxers,
>
> I am just wondering how to give a linking atom's coordinates in a qmmm
> calculation generally.
> Would it be normal to take an arithmetic average of two neighboring
> qmmm-layer-bonding at
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