On 13/06/2011 4:51 PM, vidhya sankar wrote:
Dear justin,
Thank you for your previous reply.
When i study the effect of ionic strength on stability
Which Parameter of Electrostatics Should i use? . If I use usual PME
Then will it interfere it with result?.
Dear sir,
Since the overall charge of my system is nonzero can i treat non
bonded Reaction using Set of cutoff distances
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Dear mark,
I am Typing the Literature Word, as such
Although the PME is prefered way to treat Long rang electrostatic interaction
it was not used Here Since the overall Charge of Solvated system Had non zero
value (-12) Also counter ion usually NA+ and CL- added to Neutralize th
On 13/06/2011 6:18 PM, vidhya sankar wrote:
Dear mark,
I am Typing the Literature Word, as such
Although the PME is prefered way to treat Long rang electrostatic
interaction
it was not used Here Since the overall Charge of Solvated system Had
non zero value (-12)
Google a
Hi,
Does gromacs and its associated FFs have parameters for phosphorylated
tyrosine ??
--
Bharat
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On 13/06/2011 7:15 PM, bharat gupta wrote:
Hi,
Does gromacs and its associated FFs have parameters for phosphorylated
tyrosine ??
Probably not. The best place to search is the literature.
Mark
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Hello,
I am calculating the H-bond autocorrelation using g_hbond for my
system, but after plotting
I have observed that the value for c(t) is reaching to negative, as
far as I know it can not be
negative as the probability can not be negative...please suggest
where is the problem..
--
---
Dear users,
While analyzing an MD simulation run for 100ns, for temperature,
pressure, volume and density, I got an output like this -
Energy Average Err.Est. RMSD Tot-Drift
---
Temperatu
ITHAYARAJA wrote:
Dear Sir,
Greeting!
I convey my thanks to your kind reply for rising whatever doubts and
troubles in gromacs.
I able to do my simulation with desire ligand following your
instruction. Now I am interested to simulate the dissociation of bound
ligand particularly one mol
Kavyashree M wrote:
Dear users,
While analyzing an MD simulation run for 100ns, for temperature,
pressure, volume and density, I got an output like this -
Energy Average Err.Est. RMSD Tot-Drift
-
Hi,
I have a question regarding g_dipoles. Why does g_dipoles give completely
different results of the total dipole moment, when I add or omit the energy
file? and which is correct? I mean by providing the energy file or not?
and how come I use the energy file when I want to calculate the dipole
Dear gromacs users
I need a figure of superimposed structures.
I used g_confrms -f1 1.pdb -f2 2.pdb -o fit.pdb to obtain superimposed
structures.
when I see fit .pdb using VMD, only 1 structure is seen where as I want to
have 2 structures simultaneously.
Should I use another commands or flags?
Dear Sir,
Thanks for your reply.
It means "not a number." I've never seen that before from g_energy, but
> based on the extremely small error estimates, especially for the
> temperature, I'd suspect you're using extremely tight coupling which may be
> causing some error.
I was thinking such
Dear gromacs users
I know There are two models. VMD loads them as sequential frames such
that they can be animated (frame "0" and "1").
I want to have 2 structures simultaneously and not as sequential animation.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Te
leila karami wrote:
Dear gromacs users
I know There are two models. VMD loads them as sequential frames such that they can be animated
(frame "0" and "1").
I want to have 2 structures simultaneously and not as sequential animation.
So copy and paste the two models into separate .pdb files
Kavyashree M wrote:
Dear Sir,
Thanks for your reply.
It means "not a number." I've never seen that before from g_energy,
but based on the extremely small error estimates, especially for the
temperature, I'd suspect you're using extremely tight coupling which
may be causing
Dear Justin
very thanks for your reply
as you said I have two choices : 1) copy and paste the two models into
separate .pdb files.
2) trjconv -sep .no matter which one I choose. the result is the same.
because vmd don't open two separate pdb files?
is there another way to have 2 structures simu
Dear Sir,
> What does gmxcheck tell you about the .edr file that is giving weird
> results? Do the plots look normal? Perhaps a frame got corrupted somewhere
> along the way. The screen output should print how many frames were
> considered in the analysis; if it does not match your expectations
leila karami wrote:
Dear Justin
very thanks for your reply
as you said I have two choices : 1) copy and paste the two models into
separate .pdb files.
2) trjconv -sep .no matter which one I choose. the result is the same.
because vmd don't open two separate pdb files?
Certainly VMD can
Kavyashree M wrote:
Dear Sir,
What does gmxcheck tell you about the .edr file that is giving weird
results? Do the plots look normal? Perhaps a frame got corrupted
somewhere along the way. The screen output should print how many
frames were considered in the analysis; if i
Dear Sir,
May be this protein is a disulphide bonded dimer where both the monomers
are identical and only 1 disulphide bond is there between them. But other
proteins
were not like that. May be that is the MAJOR reason for this. but strangely
temp, pres,
vol, density, kinetic, potential and tota
Kavyashree M wrote:
Dear Sir,
May be this protein is a disulphide bonded dimer where both the monomers
are identical and only 1 disulphide bond is there between them. But
other proteins
were not like that. May be that is the MAJOR reason for this. but
strangely temp, pres,
vol, density,
Dear Justin
Thanks for your attention
My problem was solved.
I have a new question. as I said my goal is superposition of averaged md
structure and x-ray structure.
My simulation is 5 ns. How to obtain the MD structure average for the period
1.5–5 ns? what command?
--
Leila Karami
Ph.D. stu
leila karami wrote:
Dear Justin
Thanks for your attention
My problem was solved.
I have a new question. as I said my goal is superposition of averaged md
structure and x-ray structure.
My simulation is 5 ns. How to obtain the MD structure average for the
period 1.5–5 ns? what command?
thanks for the reply...
Actually I have found the amber parameters for p-TYR from the following
links : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro
I am not able to how build the residue topology .. shall I add the topology
of phosphate only from this to normal tyrosine residue ??
!!
bharat gupta wrote:
thanks for the reply...
Actually I have found the amber parameters for p-TYR from the following
links : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro
I am not able to how build the residue topology .. shall I add the
topology of phosphate only from this to norma
On 2011-06-13 08:33:15AM -0500, bharat gupta wrote:
> thanks for the reply...
>
> Actually I have found the amber parameters for p-TYR from the following links
> : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro
>
> I am not able to how build the residue topology .. shall I add the topolog
Hello dear gmx-users,
I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as the
solvent ( with a positively charged protein and few DHB anions) in a box.
I have created the .itp and .gro file of DHB using PRODRG.
I am able to create the system, but when I try to energy minimiz
shivangi nangia wrote:
Hello dear gmx-users,
I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as
the solvent ( with a positively charged protein and few DHB anions) in a
box.
I have created the .itp and .gro file of DHB using PRODRG.
Unrelated advice - the topology
Dear Bharat,
You can use the Dundee PRODRG server to prepare the topology/parameter
of any structure for GROMACS or some other programs. Here is the link:
http://davapc1.bioch.dundee.ac.uk/prodrg/
you should tag the phosphate group and draw the structure of
phosphotyrosine and load it. Good Luck
sarah k wrote:
Dear Bharat,
You can use the Dundee PRODRG server to prepare the topology/parameter
of any structure for GROMACS or some other programs. Here is the link:
Be careful with PRODRG, its results are not good (posted for the second time in
15 minutes):
http://www.gromacs.org/Do
You can try also
$ git tag
release-1-6
release-1-6-01
release-2-0
release-2-0-01
release-2-0-02
release-3-0
release-3-1
release-3-1-1
release-3-1-2
release-3-1-3
release-3-1-4
release-3-2
v4.0.7
v4.5
v4.5-beta1
v4.5-beta2
v4.5-beta3
v4.5-beta4
v4.5.1
v4.5.2
v4.5.3
v4.5.4
# git checkout release-2
Dear justin,
Thank you for your previous reply.
When i study the effect of ionic strength on stability
Which Parameter of Electrostatics Should i use? . If I use usual PME Then
will it interfere it with result?.
Because My system has Non zero charge I went t
vidhya sankar wrote:
Dear justin,
Thank you for your previous reply.
When i study the effect of ionic strength on stability
Which Parameter of Electrostatics Should i use? . If I use usual PME
Then will it interfere it with result?.
Because My system has
Hello All!
I am running an MD simulation on RNA with orientation restraints. Instead of
using a single force constant for the whole trajectory, I want to start with a
very low force constant and increase it gradually and regularly up to a final
suitably high value and then continue the simulati
Hi,
The problem is that g_hbond subtracts a "background level" to compensate for
the finite size of the system. I thought that feature had been taken away,
however. Are you using old code?
Erik
12 jun 2011 kl. 19.33 skrev bipin singh:
> Hello,
>
> I am calculating the H-bond autocorrelation
Hi,
I wanted to run an atomistic simulation where I would like to constrain
helicity of a helical peptide( i.e the initial configuration is an ideal helix)
. I was wondering whether there is a way to constrain the helix dihedral angles
in Gromacs. Also, if there is any other option to keep the
Sanku M wrote:
Hi,
I wanted to run an atomistic simulation where I would like to
constrain helicity of a helical peptide( i.e the initial configuration
is an ideal helix) . I was wondering whether there is a way to constrain
the helix dihedral angles in Gromacs. Also, if there is any other
Dear gmx-users,
I am using GROMACS 4.5.4 to run a pure water system using SPC/E model
containing 32000 molecules. I have done the equilibration for 2 ns followed by
production run of 5 ns using NPT ensemble at 300K.
I am using PME for treating electrostatic interactions (cut-off 0.9 nm).
My quest
Dear Aditi:
you can do this by scripting gromacs to run in short segments,
modifying the force constant for each run. e.g.:
#!/bin/bash
for((i=1;i<=100; i++)); do
let "j=i-1"
grompp -f ${i}.mdp -p ${i}.top -f ${j}.gro -o ${i}.tpr
mdrun -deffnm ${i}
done
You only need to use some more s
Hi Justin,
Thanks so much. I really appreciate your time looking into this. Like you
said, it is hard to imagine that this could possibly be a bug. Anyway, I
will submit an issue in a few days if there are no other comments.
Andrew
--
Date: Sun, 12 Jun 2011 20:43:39 -0400
From
Hello,
I have a system with 128 emi (cations) and 128 Cl (anions).
I want to study is there any bifurcated interaction between hydrogen of
cation and CL atoms or CL atom interacting with 2 different hydrogen of
cation.
For this I considered all CL atoms are distinguishable.
I am thinking to run
On 14/06/2011 4:18 AM, Rini Gupta wrote:
Dear gmx-users,
I am using GROMACS 4.5.4 to run a pure water system using SPC/E model
containing 32000 molecules. I have done the equilibration for 2 ns
followed by production run of 5 ns using NPT ensemble at 300K.
I am using PME for treating electrost
Dear Sir,
g_mindist analysis showed the violation of minimum image convention, it
was violated over a short period of time and then it came back to normal.
I attach the plot herewith. Should this data be discarded or any useful
information
can be obtained.
Thank you
With Regards
M. Kavyashree
Hi everyone. I'm doing a simulation of a system where a peptide is linked to a
surface and an AFM tip is brought in contact to do force measurements.
The AFM tip moves very slowly (1nm/ms), so I'm simulating stationary tips at
various distances. Does anyone know the most direct measurement f
Dear users,
In one of the simulations I have run, I have transfered
it from one system to another so some data points were missing
what I should do now. how to find which data points are missing?
Thank you
With regards
M. Kavyashree
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