Hello Sir,
I have been using the new tool "gmx gangle". My actual intention is to
calculate the orientation between any two same molecules (say cholesterol)
throughout the trajectory and there are 40 cholesterol molecules. But I
couldn't calculate it. I am getting "0" as output. My command is:
gmx
Justin..
I understand the problem..
But.. How to generate a .rtp file myself..
-
Santhosh Kumar Nagarajan
MTech Bioinformatics
SRM University
Chennai
India
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On 9/23/13 5:10 PM, aixintiankong wrote:
Dear,
First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand.
when i check the charge of NAD+, I find that the distribution of charge is not correct,
the N1N atom should be positive charge but the chimera give a negati
On 9/23/13 4:04 PM, akk5r wrote:
With what was said: what do you all think of the following parameters for
Charmm 36:
rlist = 1.2
rlistlong = 1.4
vdwtype = cutoff
rvdw-switch = 1.0
rvdw = 1.2
rcouloumb = 1.2
vdw-modifier = Potential-shift-Verlet
DispCorr = No
cutoff-scheme = Verlet
rvdw-swi
Dear Vitaly,
Thank you very much for your reply. I originally asked the question because
I wasn't sure my values were from correct procedures. Now I see how I could
properly calculate binding energies with MM.
John Lee
> Dear Vitaly,
>
>
>
> Thank you for your suggestion.
>
>
Dear,
First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and
a ligand. when i check the charge of NAD+, I find that the distribution of
charge is not correct, the N1N atom should be positive charge but the chimera
give a negative. so i copy the resp charge form
http://w
On 2013-09-23 20:23, Justin Lemkul wrote:
On 9/23/13 2:08 PM, Szilárd Páll wrote:
Hi,
Admittedly, both the documentation on these features and the
communication on the known issues with these aspects of GROMACS has
been lacking.
Here's a brief summary/explanation:
- GROMACS 4.5: implicit sol
On Mon, Sep 23, 2013 at 8:08 PM, Szilárd Páll wrote:
> Hi,
>
> Admittedly, both the documentation on these features and the
> communication on the known issues with these aspects of GROMACS has
> been lacking.
>
> Here's a brief summary/explanation:
> - GROMACS 4.5: implicit solvent simulations po
With what was said: what do you all think of the following parameters for
Charmm 36:
rlist = 1.2
rlistlong = 1.4
vdwtype = cutoff
rvdw-switch = 1.0
rvdw = 1.2
rcouloumb = 1.2
vdw-modifier = Potential-shift-Verlet
DispCorr = No
cutoff-scheme = Verlet
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Hello. I was calculating the viscosity of hexane through the Gromacs
command g_energy. Three files are generated: visco.xvg, evisco.xvg and
eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but
the value does not match the experimental. I used 8 ns simulation at
equilibrium. Ho
Dr. Vitaly V. Chaban
On Mon, Sep 23, 2013 at 2:10 PM, Justin Lemkul wrote:
>
>
> On 9/23/13 6:41 AM, Dr. Vitaly Chaban wrote:
>>
>> Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely
>> get the following error:
>>
>> Select a group: 0
>> Selected 0: 'System'
>> Reading frame
Finally, I have resolved my (little) problem: I used CHARMM-GUI to constructed
the membrane, removed the TIP3 water molecules and then resolvate the bilayer
with TIP4P/2005 water molecules. The simulation seems to work.
Stephane
On 9/23/13 10:23 AM, ABEL Stephane 175950 wrote:
> Hello Justin
On 9/23/13 2:08 PM, Szilárd Páll wrote:
Hi,
Admittedly, both the documentation on these features and the
communication on the known issues with these aspects of GROMACS has
been lacking.
Here's a brief summary/explanation:
- GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu
w
On 9/23/13 10:23 AM, ABEL Stephane 175950 wrote:
Hello Justin,
Thank you for your response and your interest for my simulations ;) I am of course aware
that the "primary" water model for the CHARMM is the TIP3(S)P model.
Since, I am mainly interested to the water dynamic around DOPC molecule
Hi,
Admittedly, both the documentation on these features and the
communication on the known issues with these aspects of GROMACS has
been lacking.
Here's a brief summary/explanation:
- GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu
which is essentially mdrun + OpenMM, hence it
On 9/20/13 7:59 AM, Mark Abraham wrote:
Note that the group scheme does not reproduce the (AFAIK unpublished)
CHARMM switching scheme, either.
In case anyone is interested, the reference cited in the CHARMM papers for the
switching and shifting functions is dx.doi.org/10.1002/jcc.540150702.
Good afternoon everybody,
I'm a bit confuse about gromacs performances with implicit solvent.
I'm simulating a 1000 residues protein with explicit solvent, using both
a cpu and a gpu cluster.
With a gpu node (12 cores and 3 M2090 gpu ) I reach 10 ns/day, while
with no gpu and 144 cores I got 34 ns
Hi,
On Thu, Sep 19, 2013 at 7:19 PM, Venkat Reddy wrote:
> @Teemu Murtola: Are there any modifications to the other gmx tools? (eg:
> rdf calculation with dynamic selection...etc). I am trying to explore the
> new version.
>
Unfortunately, there are currently very few tools using the new mechan
How do GAFF and acpype work?
Mark
On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong wrote:
> Dear prof,
> can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand
> and then use acpype to generate GAFF force field parameter for the NAD+ and
> ligand?
> --
> gmx-users mailin
On 9/23/13 11:39 AM, Dr. Vitaly Chaban wrote:
Dr. Vitaly V. Chaban
On Mon, Sep 23, 2013 at 2:10 PM, Justin Lemkul wrote:
On 9/23/13 6:41 AM, Dr. Vitaly Chaban wrote:
Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely
get the following error:
Select a group: 0
Selected
Dear prof,
can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand
and then use acpype to generate GAFF force field parameter for the NAD+ and
ligand?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search th
Hello Justin,
Thank you for your response and your interest for my simulations ;) I am of
course aware that the "primary" water model for the CHARMM is the TIP3(S)P
model.
Since, I am mainly interested to the water dynamic around DOPC molecules in the
context of the different water/DOPC mesop
On Sep 23, 2013 9:08 AM, "marzieh dehghan" wrote:
>
> Hi every body
> in order to protein- ligand docking, energy minimization was done by
> GROMACS. I did the following steps for insulin pdb file:
>
> 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce
> 2- grompp -f em.mdp -c test.
On Sep 23, 2013 9:23 AM, "Jonathan Saboury" wrote:
>
> I tried minimizing a box of cyclohexanes and water. The first frame is
> fine, but after that seemingly random lines form in vmd with the
> cyclohexanes. The waters seem to minimizing just fine though.
>
> I am sure I am just doing something e
On Mon, Sep 23, 2013 at 2:40 PM, Jong Wha Lee wrote:
> Dear Vitaly,
>
>
>
> Thank you for your suggestion.
>
>
>
> I have also tried calculating interaction energies by specifying energygrps
> in .mdp file, but calculated energies deviate greatly from QM calculated
> energies and experimental resu
Dear Vitaly,
Thank you for your suggestion.
I have also tried calculating interaction energies by specifying energygrps
in .mdp file, but calculated energies deviate greatly from QM calculated
energies and experimental results. I suspect that the structure of each
component in complex diffe
On 9/23/13 6:41 AM, Dr. Vitaly Chaban wrote:
Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely
get the following error:
Select a group: 0
Selected 0: 'System'
Reading frame 0 time0.000
Precision of traj.xtc is 0.004 (nm)
Using output precision of 0.001 (nm)
Back O
On 9/23/13 5:02 AM, ABEL Stephane 175950 wrote:
Hello,
Because I want to compare the simulation results (essentially water dynamic)
with previous simulations of reverse micelles, micelles carried out with the
same water model.
The math for producing the virtual site in TIP4P is described
On 9/23/13 3:28 AM, Jonathan Saboury wrote:
That said, there is an spc.itp within the AMBER subdirectories that needs
to be
#included more explicitly, i.e. #include "amber99sb.ff/spc.itp"
May I ask why you are using SPC? The AMBER force fields were parametrized
with
TIP3P, so I see no via
On 9/23/13 3:08 AM, marzieh dehghan wrote:
Hi every body
in order to protein- ligand docking, energy minimization was done by
GROMACS. I did the following steps for insulin pdb file:
1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce
2- grompp -f em.mdp -c test.pdb -p topol.top
Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely
get the following error:
Select a group: 0
Selected 0: 'System'
Reading frame 0 time0.000
Precision of traj.xtc is 0.004 (nm)
Using output precision of 0.001 (nm)
Back Off! I just backed up confout.gro to ./#confout.gr
Hello,
Because I want to compare the simulation results (essentially water dynamic)
with previous simulations of reverse micelles, micelles carried out with the
same water model.
Stephane
--
Message: 8
Date: Mon, 23 Sep 2013 10:45:56 +0200
From: "Dr. Vitaly Chaba
I am confused. Why do you want 4-sites water?
Dr. Vitaly V. Chaban
On Mon, Sep 23, 2013 at 10:36 AM, ABEL Stephane 175950
wrote:
> Hello all,
>
> It is not a gromacs problem "per se", but I hope that some gromacs users can
> help me. I would to do simulations of phospholipid bilayers with the
Dear Jonathan -
Is it not a PBC effect? Try to display atoms as spheres - it will look
better. Otherwise, use the options in trjconv to remove PBC in the
visualized structure(s).
Dr. Vitaly V. Chaban
On Mon, Sep 23, 2013 at 9:22 AM, Jonathan Saboury wrote:
> I tried minimizing a box of cyclohe
Dear John -
I think you can achieve the goal even faster if you just define two
groups, such as MOL1 and MOL2 in MDP and then see the interaction
energy between them using g_energy.
5% is a decent agreement. Usually, even basis set superposition error
is larger (if you include this correction).
Hello all,
It is not a gromacs problem "per se", but I hope that some gromacs users can
help me. I would to do simulations of phospholipid bilayers with the TIP4P/2005
water model. I have downloaded in the Klauda's website several bilayer starting
conformations. However, since CHARMM uses the
Dear Gromacs users,
I’m trying to calculate the binding enthalpy of a host molecule with a
guest molecule in vacuum. I cannot perform QM calculations because some
systems I’m studying are too large.
I know that free energy calculations are possible with Gromacs, but they
require some cautio
>That said, there is an spc.itp within the AMBER subdirectories that needs
to be
>#included more explicitly, i.e. #include "amber99sb.ff/spc.itp"
>
>May I ask why you are using SPC? The AMBER force fields were parametrized
with
>TIP3P, so I see no viable reason to use a different water model.
Ah,
I tried minimizing a box of cyclohexanes and water. The first frame is
fine, but after that seemingly random lines form in vmd with the
cyclohexanes. The waters seem to minimizing just fine though.
I am sure I am just doing something extremely silly and I just don't know
it because of ignorance. I
Hi every body
in order to protein- ligand docking, energy minimization was done by
GROMACS. I did the following steps for insulin pdb file:
1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce
2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr
3-mdrun -v -deffnm em
4- editconf -f
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