Dear Ishrat,
I recommend this article and references therein for TMAO + urea parameters:
http://dx.doi.org/10.1021/jacs.7b11695.
Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Bi
Hi,
The urea model of Lorna Smith (
https://pubs.acs.org/doi/abs/10.1021/jp030534x
) should be compatible with GROMOS force field.
Best regards
Alessandra
On Wed, Mar 4, 2020 at 7:00 AM ISHRAT JAHAN wrote:
> Dear all,
> I want to do MD simulation of protein in urea and urea-TMAO mixture. Can
>
Dear all,
I want to do MD simulation of protein in urea and urea-TMAO mixture. Can
you suggest me which force field would be better for urea and urea tmao
mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field
as I have done the simulation of protein with this force field. Any
s
Dear all,
I want to do MD simulation of protein in urea and urea-TMAO mixture. Can
you suggest me which force field would be better for urea and urea tmao
mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field
as I have done the simulation of protein with this force field. Any
s
Den 2019-12-19 kl. 12:21, skrev Pragati Sharma:
Hello all,
I am simulating a polymer system (3 atoms, 2fs time step, PME) on a
workstation with CPU: 2X6 cores (24 logical) and 2 2080 RTX GPUs.
I am running the 2 separate simulations using 10 threads and 1 GPU each
using command:
*gmx_tmpi
Hello all,
I am simulating a polymer system (3 atoms, 2fs time step, PME) on a
workstation with CPU: 2X6 cores (24 logical) and 2 2080 RTX GPUs.
I am running the 2 separate simulations using 10 threads and 1 GPU each
using command:
*gmx_tmpi mdrun -v -deffnm md2 -nb gpu -gpu_id 1 -nt 10*
I
Hi,
I would generally not bother. You're already modelling something
unphysical. What is the consequence for your observations of either an
unexpectedly large range of position, or an uncharacteristic distribution
of KE?
Mark
On Mon., 15 Jul. 2019, 20:13 Alex, wrote:
> Dear Gromacs user,
> Usi
Dear Gromacs user,
Using flat-bottom potential I am creating a cubic box (wall) to keep some
of the molecules in a specific region of the box. I wonder if it is matter
how large or small the force constant (k_fb) be as far as the created wall
does the job well?
For instance I just chose the 4184 (K
Dear Gmx Experts,
I would like to simulate hydroxyapatite with short peptides. I would like
to use my own prepared surface which consists of a surface and a hole. I
looked for some possible parameters. INTERFACE force field is compatible
with GROMACS, which contains a number of small surfaces and
Hi,
You can use acpype to build the amber forcefield parameters. Each force
field have corresponding servers which can make .tpr file for you. You can
easily run simulation with that file.
On Mon 10 Jun, 2019, 6:43 PM antonia vyrkou, wrote:
> Dear all,
>
> I want to simulate an organometalli
Dear all,
I want to simulate an organometallic compound and how it affects an
enzyme's function using Gromacs but I am having trouble finding suitable
force field parameters. If would really appreciate any suggestions for a
Gromacs compatible , Amber compatible force field
Thank you
Antonia
--
Hello Dear Gromacs users
I need to do umbrella sampling on a single atom. Instead of doing "pulling"
simulation or umbrella sampling, I put a constraint on the atom and after
simulation I got the trajectory of that atom using VMD. The only thing that
I should check is that: Is the constraint in Gr
On 3/4/19 8:59 AM, Smith, Micholas D. wrote:
Hi Swapnil Bhujbal,
The parameters exist; however, the residue rtp file may not have entries for
the phosphorylated residues. If you want to use pdb2gmx to you will need to add
these residues into the rtp file associated with the force-field.
Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Swapnil
Bhujbal
Sent: Monday, March 4, 2019 8:12:37 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force field
Dear Users,
I'm performing ligand-protein simulation. My protein has phosphothreonine
and phosphoserine residues. So I have cheched this forum and accordingly I
have downloaded Charm36 force field November 2018 (
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) and kept in my
installation d
hey are space delimited.
Regards,
Peter
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Matthew
Stoodley
Sent: Thursday, February 21, 2019 12:59 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force field parameters not known
Hi,
I am currently trying to perform a simulation on a chemical molecular machine
but whenever I try and do the pdb2gmx command and select a force field it comes
up with the message 'the residue DVHY is not recognised'. From my understanding
what I should do is to update the residue in the speci
I am new to gromacs.
I am generating Polymers structures of varying chain length via Avogrado
software. I am not sure about how to generate the .itp file. for a specific
force field, in my case say OPLSAA.
Also in case my polymer is a poly electrolyte how do I assign charges or
how do I let the sy
users-boun...@maillist.sys.kth.se] On Behalf Of Alex
Sent: Sunday, September 30, 2018 12:44 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] force field not found
Yeah, if it is missing bonded parameters, you can always try to find
something similar, at least with OPLS-AA -- don't really know abo
12:44 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] force field not found
Yeah, if it is missing bonded parameters, you can always try to find
something similar, at least with OPLS-AA -- don't really know about the
other ff.
Alex
On 9/29/2018 8:58 PM, paul buscemi wrote:
>
Yeah, if it is missing bonded parameters, you can always try to find
something similar, at least with OPLS-AA -- don't really know about the
other ff.
Alex
On 9/29/2018 8:58 PM, paul buscemi wrote:
Alex,
I wanted to practice some more with x2top using a simple CH3 -( CH2)14 -Ch3
pdb mode
Alex,
I wanted to practice some more with x2top using a simple CH3 -( CH2)14 -Ch3
pdb model. oplsaa works fine, but not 54a7 FF generating the erro “ cannot
find forcefield for C “ Th two CH3’s do not cause the error found but the
fourteen CH2’s.
In the ffbonded.itp bond angle types i see
Read the papers for the forcefield, that will tell you how things are
parameterised.
On Sat, 15 Sep. 2018, 2:49 am RAHUL SURESH, wrote:
> Hi Users
>
> I am performing a simulation for a bonded metal-protein complex system.
> Here I am aware of adding the essential parameters in ffbonded .itp. Th
Hi Users
I am performing a simulation for a bonded metal-protein complex system.
Here I am aware of adding the essential parameters in ffbonded .itp. The
force constant value (kb) in the ffbonded.itp file is calculated using
Gaussian. I would like to clarify the method I have adopted to measure kb
Sorry for the duplicate post.
Hi Users
I am performing a simulation for a bonded metal-protein complex system.
Here I am aware of adding the essential parameters in ffbonded .itp. The
force constant value (kb) in the ffbonded.itp file is calculated using
Gaussian. I would like to clarify the meth
Hi Users
I am performing a simulation for a bonded metal-protein complex system.
Here I am aware of adding the essential parameters in ffbonded .itp. The
force constant value (kb) in the ffbonded.itp file is calculated using
Gaussian. I would like to clarify the method I have adopted to measure kb
It will be useful for all candidate including me those who don't want to
go for
calculating PMF but just want to study the stability of the
simple nucleic acid with drugs (ICL) or with protein+dsDNA or DNA aptamer
etc. during the structural transition.
Where rupture of dsDNA or unzipping of dsDNA
It can take time to read through papers. A title, link and a short
summary would be helpful to understand what the benefit would be. In
particular whether you just need information to add the functionality
for your use case or whether enough people other would use the extra
functionality you re
Dear Dr. Justin
Ultimately Mark has not replied .
Can you please tell me what this peak is revealing.
hear 3' of one strand is fixed and 3' of another strand is pulled along the
helical direction of dsDNA (12 bp). using constant velocity pulling using
your
protocol of umbrella sampling (output f/t
Hello,
I am using constant velocity method in order to pull a nanoparticle through a
lipid bilayer in water solution in Gromacs.
I should calculate the simultaneous force in order to take an integral over
position to obtain the PMF.
Do you know how can I measure the simultaneous force in order
Dear Mark,
There are several experiments have been done for protein and DNA unfolding.
Thy became pioneer in this field. That is why force should apply and
corresponding reaction
coordinates are measured . Here Gromacs login do not allow to upload larger
data.
But I can mention some paper addres
So, Dear Justin and Mark
Basically in Gromacs pulling using umbrella sampling. Force corresponding
to the distance increment
during constant velocity pulling becomes like.
F= k(vt-x)
k=spring constant
v= constant velocity
t=time
x= distance between pulled group and reference group.
The force fil
Hi,
Can you please share a link to something that indicates why this would be a
good tool for modeling such experimental pulling scenarios? Making the case
for implementing such a feature would benefit from that.
Mark
On Mon, Aug 13, 2018, 13:42 Rakesh Mishra wrote:
> Hello Mark,
>
> Thank for
On 8/13/18 6:38 AM, Rakesh Mishra wrote:
Hello Mark,
Thank for your clarification. Gromacs pulling has simple protocol for
pulling
using umbrella sampling. Where one can only get f/t and x/t . here t is
linearly
increases for both cases of force and distance. That actually not full fill
the
Hello Mark,
Thank for your clarification. Gromacs pulling has simple protocol for
pulling
using umbrella sampling. Where one can only get f/t and x/t . here t is
linearly
increases for both cases of force and distance. That actually not full fill
the need of
experimental pulling.
On Mon, Aug 13
Hi,
It's possible, but there is no code written for it.
Mark
On Mon, Aug 13, 2018, 12:47 Rakesh Mishra wrote:
> Dear Justin.
>
> Thanks for your kind advise.
> But why don't it is not possible to apply the constant force which should
> increases linearly (at each instant of time delta)
> lik
Dear Justin.
Thanks for your kind advise.
But why don't it is not possible to apply the constant force which should
increases linearly (at each instant of time delta)
like at
t1 -f1
t2-f2
.
.
tn-fn
and corresponding to that force we get extension for each increment of
time in Gromacs. This is m
On 8/9/18 6:37 AM, Rakesh Mishra wrote:
Dear all,
Can anyone shed some light as ,Is it possible to apply force/time for
pulling in gromacs. Means I want to pull my system in step wise . eg.
0 - t1 force applied f1
t1+dt to t2 force f2
t2+dt to t3 force f3
.
.
.
Dear all,
Can anyone shed some light as ,Is it possible to apply force/time for
pulling in gromacs. Means I want to pull my system in step wise . eg.
0 - t1 force applied f1
t1+dt to t2 force f2
t2+dt to t3 force f3
.
.
.
tn-1 +dt to tn force fn
Is it possible.
N
I have already mailed them... waiting for their reply..
On Sat, 7 Jul 2018, 11:22 pm Mark Abraham, wrote:
> Hi,
>
> Your other good approach is to contact the authors to ask them to share
> their methodology fully, ie force field files.
>
> Mark
>
> On Sat, Jul 7, 2018, 13:47 Soham Sarkar wrote
Hi,
Your other good approach is to contact the authors to ask them to share
their methodology fully, ie force field files.
Mark
On Sat, Jul 7, 2018, 13:47 Soham Sarkar wrote:
> Dear All,
> Can anyone please tell me, where from I get the parameters for
> Osmotic, Kast, Netz force f
Dear All,
Can anyone please tell me, where from I get the parameters for
Osmotic, Kast, Netz force field like the files OPLS, CHARMM which is
already in GROMACS? I have got the files for the KBFF force field but not
these three. The paper by Dias and group
https://journals.aps.org/prl
On 6/19/18 4:35 PM, Wahl, David M wrote:
Hello,
I am working on a molecular dynamics simulation in GROMACS and am curious as to
which force field will be the best to run a simulation on a small organic
molecule containing carbon, nitrogen, oxygen and hydrogen. Through some
research it se
I think you should recalculate charged of atoms of that molecule, the other
properties can used from GAFF
URL: https://qvu.netlify.com/#/
On Wed, Jun 20, 2018 at 3:36 AM Wahl, David M wrote:
> Hello,
>
>
> I am working on a molecular dynamics simulation in GROMACS and am curious
> as to which f
I think you should recalculate charged of atoms of that molecule, the
other properties can used from GAFF
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* Can't post? Read http://www.gromacs.org/Support/M
Hello,
I am working on a molecular dynamics simulation in GROMACS and am curious as to
which force field will be the best to run a simulation on a small organic
molecule containing carbon, nitrogen, oxygen and hydrogen. Through some
research it seems that the general Amber force field (gaff)
Hi,
i am trying to parametrize a Metal-Organic-Framework for later gromacs
simulations. Does anybody have experience in deriving parameters like
force constants completely from theory? I know that there are techniques
doing it with DFT-calculations but i would like to know other methods as
we
Hi,
Posting just before a weekend isn't all that likely to get a quick reply...
;-) Note that your 2, 3, and 4 have Si-O-Si angles (and related dihedrals)
which isn't found in 1, so you clearly cannot take the parameters for 1 and
construct a complete topology for 2, 3, and 4. So you still have th
Any idea, please?
Cheers,
Alex
On Fri, Apr 27, 2018 at 5:50 PM, Alex wrote:
> Dear all,
> I have the Gromos-54A7 force fields (FF) for the molecule number 1 in the
> below link, using thoes how I can have the FF for the molecules number 2,3
> and 4 in the same link without doing extra calculatio
Dear all,
I have the Gromos-54A7 force fields (FF) for the molecule number 1 in the
below link, using thoes how I can have the FF for the molecules number 2,3
and 4 in the same link without doing extra calculations? What could be the
relation between the FF of other molecule with the FF of molecule
Hi,
You can't "get bonded parameters and force constants" unless you have
chosen the potential functions in which they will work.
Mark
On Wed, Apr 25, 2018 at 12:49 PM Momin Ahmad wrote:
> Hi Mark,
>
> thanks for the answer. My thought was if i get all bonded parameters and
> force constants t
Hi Mark,
thanks for the answer. My thought was if i get all bonded parameters and
force constants through DFT-calculations i should be able to choose my
preferred potential equations. Or am i wrong because i am still using
nonbonded data from UFF?
Cheers
Momin
Am 25.04.2018 um 12:12 schrieb
Hi,
The parameters are strongly correlated to both the equations in which they
work, and the other parameters in the force field alongside which they were
parametrized. Many kinds of transfer simply will not work, and all of them
need to be validated, e.g. by reproducing some previous computationa
Hi,
i have a question regarding force fields (not gromacs related). In UFF
(https://pubs.acs.org/doi/abs/10.1021/ja00051a040) the potential
equations of angles and dihedrals are different than in gromacs. OBGMX
just reparametrizes them to still use the data from UFF
(https://onlinelibrary.wil
On 4/13/18 6:26 AM, rose rahmani wrote:
Hello,
I use AMBER force field.
So, how about periodic structures? like inorganic nanosheet and nanotubes?
One would never attempt to do parametrization directly on a full,
periodic structure, largely because (1) it's not possible/practical and
(2) y
Hello,
I use AMBER force field.
So, how about periodic structures? like inorganic nanosheet and nanotubes?
Thank you so much
On Fri, 13 Apr 2018, 14:50 Paul bauer, wrote:
> Hello,
>
> this depends on the force field you are using. Some of them use
> parameters from a QM optimization and partia
Hello,
this depends on the force field you are using. Some of them use
parameters from a QM optimization and partial charge calculation.
But even then you need to be careful that the results from the QM are
not just random numbers :)
But I'm not sure myself how I would tackle something like M
On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote:
> Hello,
>
> I would recommend that you check relevant publications for the
> simulation of magnetite if people have tried to simulate it in solvent.
> I could not find anything during a short search, but maybe you'll be
> more successful. :)
> If the
Hello,
I would recommend that you check relevant publications for the
simulation of magnetite if people have tried to simulate it in solvent.
I could not find anything during a short search, but maybe you'll be
more successful. :)
If there are no published parameters in the literature you will
Dear gromacs users,
I want to simulate a protein in different concentration of Fe3O4.
How to obtain force field parameters of Fe3O4?
Any help will highly be appreciated.
Best,
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_
which requires a
separate calculation, performed by gmx distance. Then, one can assemble
the plot that was shown in the paper.
-Justin
Parthiban Marimuthu.
Message: 1
Date: Fri, 23 Mar 2018 16:10:45 +0100
From: Joe Jordan
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force displacement cur
: 1
> Date: Fri, 23 Mar 2018 16:10:45 +0100
> From: Joe Jordan
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Force displacement curve in SMD simulation
> Message-ID:
> com>
> Content-Type: text/plain; charset="UTF-8"
>
> Try reading the me
Try reading the methods section of the paper. I looked for ~45 seconds and
found it.
On Fri, Mar 23, 2018 at 4:02 PM, Parthiban Marimuthu
wrote:
> Hello,
>
> Can any one suggest how to calculate the force-displacement curve as shown
> in figure 4B in https://pubs.acs.org/doi/full/10.1021/ci10034
Hello,
Can any one suggest how to calculate the force-displacement curve as shown
in figure 4B in https://pubs.acs.org/doi/full/10.1021/ci100346s for steered
molecular dynamics simulation.
Regards, P.M.
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On 1/15/18 1:27 PM, Harsha Ravishankar wrote:
Hello Justin,
Thanks for the reply. I only make use of Charmm GUI to generate the
membrane patch, as I need to orient my protein in a particular orientation.
However when I made use of the .itp forcefield files in gmx grompp -f
ions.mdp -c solvate.
Hello Justin,
Thanks for the reply. I only make use of Charmm GUI to generate the
membrane patch, as I need to orient my protein in a particular orientation.
However when I made use of the .itp forcefield files in gmx grompp -f
ions.mdp -c solvate.gro -p topol.top -o ions.tpr I get errors stating
On 1/15/18 9:45 AM, Harsha Ravishankar wrote:
Dear All,
I am a beginner with Gromacs and simulations and I want to simulate a
membrane and protein complex with the membrane comprising of 5 different
lipid molecules. The membrane was generated with Charmm-GUI and the
appropriate Gromacs paramet
Dear All,
I am a beginner with Gromacs and simulations and I want to simulate a
membrane and protein complex with the membrane comprising of 5 different
lipid molecules. The membrane was generated with Charmm-GUI and the
appropriate Gromacs parameters for the different lipids were also obtained.
Hi,
There's lots of discussion in the reference manual, and also in the force
field files themselves.
Mark
On Mon, Jan 8, 2018 at 4:28 PM Lara rajam wrote:
> Dear GMX users
> I would like to know where we would get the force field information in GMX
> .
> Like in NAMD the Topology and parm fil
>I would like to know where we would get the force field information in GMX
The answer is obvious: read manual (chapter 4 I"nteraction function and force
fields" and 4.10 "Force field"). The FF files are situated in
/usr/share/gromacs/top (for my PC) and are transparent enouth.
--
Gromacs Us
Dear GMX users
I would like to know where we would get the force field information in GMX
.
Like in NAMD the Topology and parm file tells the details of the atom
labeling,charge,connectivity etc., Simillarly where I could see the Gromos
force field insights.
Please provide me links or tutorials tha
Hi,
Thanks for the tip, I brought the website back up. Most of the relevant
force fields are in the repo, however.
Mark
On Mon, Dec 4, 2017 at 7:54 PM Zahedeh Bashardanesh
wrote:
> Hi,
>
> Does anybody know where else to get the reliable amber force field package
> for gromacs except from grom
Hi,
Does anybody know where else to get the reliable amber force field package
for gromacs except from gromacs website? The webpage has been down since
Saturday.
Best,
---
Zahedeh Bashardanesh, Ph.D. Candidate
Dep
Thanks a lot Justin!
Best regards
On Thu, Nov 16, 2017 at 2:31 PM, Justin Lemkul wrote:
>
>
> On 11/16/17 8:28 AM, Faezeh Pousaneh wrote:
>
>> Hi
>>
>> sorry for silly question, but I did not find my answer by searching.
>>
>> In gromos force fields, the file nonbonded.itp includes nonbonded
On 11/16/17 8:28 AM, Faezeh Pousaneh wrote:
Hi
sorry for silly question, but I did not find my answer by searching.
In gromos force fields, the file nonbonded.itp includes nonbonded
parameters for two different atoms, e.g
C O 1 2.300953E-03 2.222000E-06
while I do not see oplsaa provides pa
Hi
sorry for silly question, but I did not find my answer by searching.
In gromos force fields, the file nonbonded.itp includes nonbonded
parameters for two different atoms, e.g
C O 1 2.300953E-03 2.222000E-06
while I do not see oplsaa provides parameters for nonbonded interactions of
different
Hi Justin,
just for testing, I applied cgenff_charmm2gmx.py with
charmm36-nov2016.ff as it has the same CGenFF version:
--Version of CGenFF detected in
/usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/forcefield.doc
: 3.0.1
But I still get the same warnings and errors.
Would you s
On 11/3/17 10:33 AM, Hermann, Johannes wrote:
Hey Justin,
thanks - again - for your reply!
Now I get duplicated parameters warnings and errors:
WARNING 1 [file fmn.prm, line 5]:
Overriding Bond parameters.
old: 0.1295 405848 0.1295
405848
n
Hey Justin,
thanks - again - for your reply!
Now I get duplicated parameters warnings and errors:
WARNING 1 [file fmn.prm, line 5]:
Overriding Bond parameters.
old: 0.1295 405848 0.1295
405848
new: CG2R64 NG2D1 1 0.1414 255224.0
On 11/3/17 8:17 AM, Hermann, Johannes wrote:
Dear Justin,
thanks for the hint with the CHARMM-formatted topology and parameter
files! That is great help! I had a different atom number compared to
NAI and NADH because I had a different (non-physical) protonation
state. The text drawing help
Dear Justin,
thanks for the hint with the CHARMM-formatted topology and parameter
files! That is great help! I had a different atom number compared to NAI
and NADH because I had a different (non-physical) protonation state. The
text drawing helped me a lot to figure out the few Nomenclature
d
On 11/2/17 12:05 PM, Hermann, Johannes wrote:
Dear Justin, dear all,
thank you for your reply. I will test the web server when I have
managed to generate the mol2 file for FMN.
I had a look in the rtp file of charmm36 ff and I detected that there
are three "NADHs": NAD1 , NAI, and NAD1. N
Dear Justin, dear all,
thank you for your reply. I will test the web server when I have managed
to generate the mol2 file for FMN.
I had a look in the rtp file of charmm36 ff and I detected that there
are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code
for the reduced form
As far as I see others just replace selenium with sulphur, convert of
selenomethionine to methionine
like:https://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-14-775
On Wednesday, November 1, 2017, 8:24:10 AM GMT+2, Seera Suryanarayana
wrote:
Dear gromacs users,
I have
Dear gromacs users,
I have to do simulations for a peptide which has the selinomethionine. But
regular force fields from gromacs has no information for this residue.
kindly give me information if is there any force field for
selinometheoinine.
Thanks in advance
Surya
Graduate student
India.
--
G
On 10/30/17 10:58 AM, Hermann, Johannes wrote:
Dear all,
I want to simulate a complex consisting of a protein, FMN, and NADH. I
have two problems/questions:
1) In the "CHARMM36 all-atom force field (March 2017)" parameters for
NADH are present. But apparently I am using a wrong atom naming
Dear all,
I want to simulate a complex consisting of a protein, FMN, and NADH. I
have two problems/questions:
1) In the "CHARMM36 all-atom force field (March 2017)" parameters for
NADH are present. But apparently I am using a wrong atom naming
convention (I copied / pasted NADH from a pdb en
Hi!
I acetylated K40 my heterodimer's PDB file using PyTMs in PyMOL. Now I need
to simulate it using GROMACS. Which force field would be the best for this
purpose?
Thank you in advance!
Regards,
Raag
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On 05/04/17 16:09, Phillip Rauscher wrote:
Thanks so much for the reply Mark! For my own curiosity, is there a way
that people generally deal with neutral sp3 Nitogens? They're chiral
centers on simulation time scales, but on macroscopic scales pyramidal
inversion eliminates that.
If we take am
I see, thanks for your help!
On Wed, Apr 5, 2017 at 9:27 AM, Mark Abraham
wrote:
> Hi,
>
> The protonation state is a decision you make in setting up the topology
> (what pH am I modelling?). Having done so, you get whatever amine model the
> force field specifies, and I expect that no force fie
Hi,
The protonation state is a decision you make in setting up the topology
(what pH am I modelling?). Having done so, you get whatever amine model the
force field specifies, and I expect that no force field has such a planar
amine, because none actually have the improper dihedral you suggest they
Thanks so much for the reply Mark! For my own curiosity, is there a way
that people generally deal with neutral sp3 Nitogens? They're chiral
centers on simulation time scales, but on macroscopic scales pyramidal
inversion eliminates that.
On Wed, Apr 5, 2017 at 1:16 AM, Mark Abraham
wrote:
> H
Hi,
Amide nitrogen atoms are trigonal planar because the group is planar.
There's no free rotation about the n-c bond, and the lone pair forms a
hybrid orbital with the carbonyl.
Mark
On Tue, 4 Apr 2017 18:05 Phillip Rauscher wrote:
> It occurs to me that an example would be helpful. Here is
It occurs to me that an example would be helpful. Here is an excerpt from
the OPLS aminoacids.rtp file detailing alanine:
*[ ALA ] [ atoms ] Nopls_238 -0.500 1 Hopls_241
0.300 1 CAopls_224B 0.140 1 HAopls_140
0.060 1
Hello all,
I've noticed that in some of the force fields (in the aminoacid.rtp files),
an improper dihedral is applied to the nitrogens in the peptide bond (and
sometimes other amine groups as well), which are all sp3 hybridized with
one lone pair. Interestingly, the dihedral potential parameters
Hi,
gmx select will let you make index groups according to geometric criteria,
which will allow you to set up something like a piston of water. But of
course the molecules will diffuse, so you will want to periodically stop
the simulation, and re-build the index group for the next call to grompp.
Dear Mark
Thanks for your response. Now I have understood. Next I have created a
layer of water molecules above a graphene layer. How I can make two groups
of water say water at the topmost layer with 1.4nm thickness and rest of
the water molecules up to graphene surface.
Thanks in advance
Warm
Hi,
This is what pull groups do in GROMACS.
Mark
On Fri, 24 Feb 2017 14:37 Rana Ali wrote:
> Dear users
>
> We were running MD system consists of ion and water through a nanotube
> under a pressure gradient.
> For that we are applying pressure in terms of force to the molecules.
> Could any bo
Dear users
We were running MD system consists of ion and water through a nanotube
under a pressure gradient.
For that we are applying pressure in terms of force to the molecules.
Could any body help how to create group so that the external force will be
applied only on water molecules not on the i
Dear users
We were running MD system consists of ion and water through a nanotube
under a pressure gradient.
For that we are applying pressure in terms of force to the molecules.
Could any body help how to create group so that the external force will be
applied only on water molecules not on the i
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