You can use gmx energy (g_energy). Follow the online manual at
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-energy.html
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Dear Mario,
You can calculate NH order parameter (or any other bond order parameter) by
following method
https://extras.csc.fi/chem/courses/gmx2007/analysis/
However I was curious about gmx chi which was supposed to give dihedral
order parameter.
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Hi Everyone,
Is the S2max and S2min produced by gmx chi is same as Ss (slow order
parameter)and Sf (fast order parameter) respectively. If not may anybody
please explain what are those (S2max and S2min).
Thanks a lot.
Sincerely
Tushar
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Hi all,
I wish to use GROMOS54a6oxy forcefield parameterized by Horta et. al.
However, I am unable to find any link to download the same. It will be a
great help if any one send me the link or the forcefield.
Thanks a lot.
Tushar
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htt
me how to
assign correct partial charges.
Thanks a lot for the help.
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Hi Everyone,
I want to use LJ interaction cutoff at 12 Å and treat LJ smoothly between
10 and 12 Å. Does the following in .mdp file reflect the same?
rvdw-switch = 0.2
rvdw = 1
Kindly Reply.
Thanks a lot.
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Ph D Student
Hi Mark,
Thanks a lot for the suggestion. I will try it.
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cos (52.26 deg) * 0.09572 nm]
; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
[ virtual_sites3 ]
; Vsite fromfunctab
412310.128012065 0.128012065
Thanks a lot.
On Wed, Feb 21, 2018 at 10:48 AM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com&
hough parameters are mentioned). I have experimental data to verify if
the water model is not appropriate. It will be a great help if you can help
me getting/creating the topology.
Thanks a lot for your suggestion.
On Tue, Feb 20, 2018 at 10:00 PM, Tushar Ranjan Moharana <
tusharranjanmohar...@g
Hi All,
I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone let
me know where can I get the corresponding .itp file.
Thanks a lot.
"A society with free knowledge is better than a society with free food"
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You can do that by g_energy (or gmx energy). but before that you have to
create separate energy group and mention in .mdp file prior to md run. or
you can rerun the trajectory with above changes.
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nergy also
let me know.
Thanks a lot.
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Thanks a lot Justin.
On Wed, Aug 9, 2017 at 1:33 AM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:
> Hi All,
> I want to calculate interaction between 2 energy groups, which were not
> defined during the run. So I want to rerun and include both the energy
and by mistake the .gro and .cpt file got
overridden. Kindly suggest if there is any way to achieve the above
things.
Thanks a lot.
"A society with free knowledge is better than a society with free food"
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B. Tech, NIT Warangal
Ph D Student, CCMB
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Hi Justin,
Thanks a lot for the valuable advice.
"A society with free knowledge is better than a society with free food"
On Fri, Jul 7, 2017 at 3:04 PM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:
> Hi Justin,
> Thanks a lot for the advice. It lo
your time and effort.
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r valuable time and efforts.
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environment?
Kindly help me understand the above.
Thanks a lot
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0.14510 306165.0
1 10 1 0.10930 287014.9 0.10930 287014.9
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nsteps, if I want to rerun only the
second xtc.
2) Can I combine them to get a continuous xtc file.
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are added to mimic the
reaction condition.
Thanks a lot for your advice.
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ht
the mutant.
Here is a paper where Seifollah *et al*. have done a similar work. The work
I want to do is simpler as it doesn't involve membrane.
http://www.ncbi.nlm.nih.gov/pubmed/25427619
Thanks a lot.
"A society with free knowledge is better than a society with free food"
Tushar
.
Thanks a lot.
"A society with free knowledge is better than a society with free food"
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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[file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Thanks a lot for the help.
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Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Stude
assert len(atoms1) == len(atoms2), "%s -> %s" % ( '-'.join( map(lambda
a: a.name, atoms1)),'-'.join( map(lambda a: a.name, atoms2)) )
Thanks a lot.
"A society with free knowledge is better than a society with free food"
Tushar Ranjan Moharana
B. Tech, NIT Wara
d"
Tushar Ranjan Moharana
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Hi SAKO MIRZAIE,
Thanks for your reply. But how can we calculate difference in folding free
energy by doing 2 separate simulations? Please clarify (at least give some
hints or references).
Thanks a lot.
"A society with free knowledge is better than a society with free food"
--
Tus
irect way (like pdb2gmx or any
other program). If not then can any body explain me the way to do so(I can
write perl script if necessary).
Thanks a lot for your time and effort.
"A society with free knowledge is better than a society with free food"
Tushar Ranjan Moharana
B. Tech, NIT Wa
for your valuable advice.
"A society with free knowledge is better than a society with free food"
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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ge is better than a society with free food"
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B. Tech, NIT Warangal
Ph D Student, CCMB
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extracted by gmx energy
(g_energy).
Thanks a lot for the help.
"A society with free knowledge is better than a society with free food"
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Hi Peter,
Try this whenever opening a new terminal
source /path/to/gromacs/bin/GMXRC
What ever version you want to use mention corresponding path.
"A society with free knowledge is better than a society with free food"
Best Regards
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph
Hi Andrea,
Thanks for your precious advice.
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number of solvent molecule within 0.4 nm. However nothing
correlated with observed shift (correlation coefficient less than 0.02).
Any advice is precious and I am thankful for the same.
"A society with free knowledge is better than a society with free food"
Tushar Ranjan Moharana
B.
Hi everyone,
I am really confused between explicit and implicit solvent model. Any good
resource will be helpful to me. I am using CHARMM forcefield and TIP4P
water model. I guess it is explicit water model. Can anyone correct me?
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
with free knowledge is better than a society with free food"
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B. Tech, NIT Warangal
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x27;t succeed. Can
anybody kindly suggest me which analysis tool will be useful for me.
Thanks a lot in advance.
"A society with free knowledge is better than a society with free food"
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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* Pl
/s/y9ia804dh0766pe/energy_groups.dat?dl=0
Thanks alot for your time and consideration.
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Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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a society with free food"
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ciety with free knowledge is better than a society with free food"
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Ph D Student, CCMB
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;
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ciety with free knowledge is better than a society with free food"
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valuable time.
[image: Inline image 1]
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and effort.
Tushar Ranjan Moharana
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Ph D Student, CCMB
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am just curious to know
which force field and water model one should use for simulating a system
(preferably protein in water) at different salt concentration to see the
effect of salt concentration on the structure of the protein.
Thanks a lot for your time and advice.
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lated using GROMACS please let me know how.
Tushar Ranjan Moharana
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Ph D Student, CCMB
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PRODRG generate topology for GROMOS force field (united atom) that's too
with wrong charge. GROMOS force field doesn't consider non polar hydrogen.
If you want to use GROMOS force field, then just go ahead without counting
hydrogen.
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Stu
Hi Ming
Use *-pbc mol* while using trjconv. Anyway it is not another box.
Best Regards
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riodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = no
Any suggestion is most welcome.
Thanks for your valuable time and suggestion.
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d removing subsequent line.
Please help me in solving the problem. Thanks a lot.
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* Can't
help me in solving the problem. Thanks a lot.
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loup1up2 weight
So what do you suggest me to do?
Thanks in advance.
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Ph D Student, CCMB
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1 0.025981 0.2259811.22598 1 1012
164 1 0.0259023 0.225902 1.2259 1 1112
165 1 0.122624 0.3226241.32262 1*
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Hi Justin,
Thanks for your valuable suggestion. I ignored the hydrogen and added
manually bu -his flag.
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Ph D Student, CCMB
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while sorting
atoms". I can remove the error by adding -ignh but my concerned is this may
change the protonation state. Please help me with your valuable
suggestion.
Thanks for your time and effort.
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Hi Justin,
Thanks for your valuable suggestion. Now my problem got solved.
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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* Can't
after energy
minimization was positive (order of 10^2) in this case too.
Any suggestion to try is most welcome.
Thanks for your time and effort.
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B. Tech, NIT Warangal
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r DHA) and any other
modification I shall do to any file of that forcefield.
Any help or advice will be precious to me
Thanks for your time and effort
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