The constant angle has a weird units of kJ /mol rad^n while the angle is in
degrees. Does not make sense but at least I know where I made a mistake...
On Wed, Jun 12, 2013 at 10:43 PM, Justin Lemkul wrote:
>
>
> On 6/12/13 10:01 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> I run a simul
Dear all,
I am using charmm27 forcefield in gromacs for performing all atom simulations
(system comprising of DOPC, cholesteryl ester and protein) .I got the itp file
for dopc from the lipid book in which they have mentioned #include
"charmm27.ff/ffbonded.itp" and "charmm27.ff/ffnonbonded.it
Thank JW so much :-)
On Wed, Jun 12, 2013 at 10:30 PM, JW Gibbs wrote:
> Hi,
>
> Please see the following links:
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/
>
> http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html
>
> I think you will understa
On 6/12/13 10:01 AM, Steven Neumann wrote:
Dear Gmx Users,
I run a simulation with quartic angle potential. These function has two
minima at 100 at 120 degrees. However, seems from my simulation that it is
not applied... all angles are around 180 degrees and my chain is a line
chain (straight)
On 2013-06-11 23:31, Jeffery Perkins wrote:
or should i be doing < U+*ref_p > = ?
More specifically, + *ref_p = H
isn't really meaningful thing. I mean, you can define something
such that = H, but that's not really thermodynamics.
sorry I always have issues deciding how to talk about
Hi Guys, sorry I replay so late,
the annealing_npoints should be 4 4 4, which I incorrectly defined to 3 3 3.
the problem solved.
Thanks! Justin
On Tue, Jun 11, 2013 at 6:36 AM, Dr. Vitaly Chaban wrote:
> On Tue, Jun 11, 2013 at 12:52 PM, Justin Lemkul wrote:
>
> >
> >
> > On 6/11/13 1:11 AM,
Hi,
Please see the following links:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/
http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html
I think you will understand the concept of the pulling force once you go
through either of the links.
It's basical
Thanks Justin and Professor Shirts. The gmxdump on the resulting tpr did
indeed solve a lot of my problems. Thanks again.
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Dear Gmx Users,
I run a simulation with quartic angle potential. These function has two
minima at 100 at 120 degrees. However, seems from my simulation that it is
not applied... all angles are around 180 degrees and my chain is a line
chain (straight).
I have in my topology
[ angles ]
; i j k
Dear users,
What is the algorithm of umbrella sampling simulation ? And can anyone who
had experience in this explain pulling force to me ?
Thankul and regards,
~Thu
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Sounds like either you're following wrong instructions, or not following
them correctly. Please double check and/or take up the issue with the
author.
Mark
On Wed, Jun 12, 2013 at 3:03 PM, Revthi Sanker wrote:
> Dear all,
> I am using charmm27 forcefield in gromacs for performing all atom
> sim
Dear all,
I am using charmm27 forcefield in gromacs for performing all atom simulations
(system comprising of DOPC, cholesteryl ester and protein) .I got the itp file
for dopc from the lipid book in which they have mentioned #include
"charmm27.ff/ffbonded.itp" and "charmm27.ff/ffnonbonded.itp"
On Wed, Jun 12, 2013 at 12:42 AM, sirishkaushik wrote:
> Note that this works fine with 4.5.5.
>
> when I installed using:
>
> ./configure CPPFLAGS="-I/home/kaushik/fftw-new/include"
> LDFLAGS="-L/home/kaushik/fftw-new/lib" --enable-mpi --prefix
> /home/kaushik/gromacs_executable/gromacs-old
>
>
On 6/12/13 8:16 AM, Steven Neumann wrote:
So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions
Mark already told you this - interactions that exist are different from possible
interactions. You may have 57 interactions, but that's specific to your system
because of
So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions
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On 6/12/13 8:01 AM, Steven Neumann wrote:
60 types of atoms and 60 atoms in total belonging to one residue
The number of possible combinations is (N(N+1))/2, thus you get 1830 from 60
atom types.
-Justin
On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham wrote:
How many atom *types* are t
60 types of atoms and 60 atoms in total belonging to one residue
On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham wrote:
> How many atom *types* are there?
>
>
> On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann >wrote:
>
> > and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"
How many atom *types* are there?
On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann wrote:
> and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"
>
>
> On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann >wrote:
>
> > "All possible interactions = 60*60/2 = 1800. Where grompp take
Thanks Erik
On 06/12/2013 01:50 PM, Erik Marklund wrote:
Hi,
No, I'm afraid not. pull-dim not only determines what components are to be
printed, it also determines in what dimensions the force is to be applied
during the simulation.
Erik
On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez
wro
and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"
On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann wrote:
> "All possible interactions = 60*60/2 = 1800. Where grompp takes another 30
> from?
>
>
> On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham
> wrote:
>
>> "Parameters f
"All possible interactions = 60*60/2 = 1800. Where grompp takes another 30
from?
On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham wrote:
> "Parameters for possible interactions" is not the same as "interactions."
> The latter depend on the configuration and cut-offs... grompp is not doing
> a neig
"Parameters for possible interactions" is not the same as "interactions."
The latter depend on the configuration and cut-offs... grompp is not doing
a neighbor search!
Mark
On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann wrote:
> On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham >wrote:
>
> > gro
Hi,
No, I'm afraid not. pull-dim not only determines what components are to be
printed, it also determines in what dimensions the force is to be applied
during the simulation.
Erik
On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez
wrote:
> Dear Gromacs Users,
>
> I runned and Umbrella Sampli
On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham wrote:
> grompp is just enumerating the possible combinations of parameters given
> your inputs. Whether any of those will be used in the simulation will
> depend on whether atoms of given types are close enough and not excluded.
>
> Mark
I understa
grompp is just enumerating the possible combinations of parameters given
your inputs. Whether any of those will be used in the simulation will
depend on whether atoms of given types are close enough and not excluded.
Mark
On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann wrote:
> I got it. Howev
An why do I have 1830 non bonded? 60*60/2 = 1800. There are 57 of 1-4
combinations so it should be lower than 1800...
And why 1830 1-4 interactions as I have only 57... Please, help/
Steven
On Wed, Jun 12, 2013 at 11:40 AM, Steven Neumann wrote:
> I got it. However,
>
> I have 60 atoms in my c
Dear Gromacs Users,
I runned and Umbrella Sampling simulation but I made a mistake in the
value of the pull_dim option, so gromacs printed the z component of the
force instead of the x component that i need (with the option -pf of
mdrun). I have all files from the simulation.
Is there a way to
My current Gromacs version is 4.5.5
I think using the first option will be easy and quick.
On Wed, Jun 12, 2013 at 4:41 PM, Erik Marklund wrote:
> You have (at least) two easy options.
>
> 1) Install old_dssp that is available through the dssp web page.
> 2) Install a newer version of gromacs t
You have (at least) two easy options.
1) Install old_dssp that is available through the dssp web page.
2) Install a newer version of gromacs than you have at the moment. What version
do you currently use?
Erik
On 12 Jun 2013, at 12:56, Nikunj Maheshwari wrote:
> Yes I checked. do_dssp has n
Yes I checked. do_dssp has no -ver option.
I also found out this link
https://gerrit.gromacs.org/#/c/687/
but dont know how to install/use it.
Or maybe I can install DsspOld and see?
On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund wrote:
> Search again. The syntax for invoking dssp changed a
Search again. The syntax for invoking dssp changed at some point and it took a
while before do_dssp adapted to that. If your do_dssp is lacking the -ver
option then I'm quite confident that it uses the old syntax, which doesn't work
with the newer versions (v. 2.0+ I think) of dssp.
Erik
On 1
I got it. However,
I have 60 atoms in my chain all with given C6 and C12 with a combination
rule 1. When running grompp:
Generated 1830 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1830 of the 1830 1-4 parameter combinations
Excluding 3 bonded ne
The location of dssp is /usr/local/bin/dssp
On Wed, Jun 12, 2013 at 3:43 PM, Mark Abraham wrote:
> Right. And what is its location?
> On Jun 12, 2013 11:17 AM, "Nikunj Maheshwari"
> wrote:
>
> > Yes I did searched. But for most people, there were issues regarding the
> > path or wrong DSSP.
> >
You've got a test case that shows your tables do what you think they do,
right? I would vary this setting and expect to see no effect.
Mark
On Jun 12, 2013 10:03 AM, "Steven Neumann" wrote:
> Whether it would be that easy i will find it. I specified my own potential
> (not LJ) - so how come I sh
Right. And what is its location?
On Jun 12, 2013 11:17 AM, "Nikunj Maheshwari"
wrote:
> Yes I did searched. But for most people, there were issues regarding the
> path or wrong DSSP.
> DSSP runs for me, but do_dssp does not.
>
>
> On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund
> wrote:
>
> > Hi,
On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul wrote:
>
>
> On 6/12/13 6:00 AM, Steven Neumann wrote:
>
>> Thank you. That means that e.g. when two LJ atoms of a different type
>> approaching each other the non bonded LJ potential energy is a sum of two
>> potentials of those atoms?
>>
>>
> No,
I appologise with the below, I got entropy and enthalpy confused for a mement. Funny.
Stephan
Gesendet: Dienstag, 11. Juni 2013 um 23:54 Uhr
Von: "lloyd riggs"
An: "Discussion list for GROMACS users"
Betreff: Aw: [gmx-users] Enthalpy Confusion
If you only want the total for the syst
On 6/12/13 6:00 AM, Steven Neumann wrote:
Thank you. That means that e.g. when two LJ atoms of a different type
approaching each other the non bonded LJ potential energy is a sum of two
potentials of those atoms?
No, please refer to the Gromacs manual for discussion on "combination rules" an
Thank you. That means that e.g. when two LJ atoms of a different type
approaching each other the non bonded LJ potential energy is a sum of two
potentials of those atoms?
On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul wrote:
>
>
> On 6/12/13 5:30 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
On 6/12/13 5:30 AM, Steven Neumann wrote:
Dear Gmx Users,
Please, correct me if I am wrong. In ffnonbonded.itp
[ atomtypes ] - these are nonbonded parameters between atoms of the same
type
No, these are the nonbonded parameters that are used when applying combination
rules between any atom
On 6/12/13 4:52 AM, Colin Bannister wrote:
Chandan,
I was looking at :
http://manual.gromacs.org/online/getting_started.html#setup
Which mentions these files. Is this wrong ?
Yes, it is. Several pages in the online manual are outdated, and share/tutor
was removed some time ago because
On 6/12/13 12:10 AM, maggin wrote:
Hi, Justin,
You are right, I should first fix the bad geometry.
I check 1dx0.pdb, and the problematic areas are:
atom1 atom2
1 N1+ (GLY124 N) 4 H (GLY124 HT3)
181 C (PRO137 CD)182 H
Dear Gmx Users,
Please, correct me if I am wrong. In ffnonbonded.itp
[ atomtypes ] - these are nonbonded parameters between atoms of the same
type
[ nonbond_params ] these are nonbonded parameters between atoms of
different type
[ pairtypes ] - 1-4 interactions
If that is correct why amber force
Dear all,
I'm using Gromacs 4.5.5 with the amber ff99SB forcefield to run NVE
simulations on ethane in 725 TIP3P water molecules. I used antechamber
to parametrise my ethane.
I have 2 issues;
Firstly the energy conservation of my simulations seems to get worse as
I lower my timestep, here is an
Yes I did searched. But for most people, there were issues regarding the
path or wrong DSSP.
DSSP runs for me, but do_dssp does not.
On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund wrote:
> Hi,
>
> Search the mailing list. This problem and its solution has been repeatedly
> discussed.
>
> Erik
>
Chandan,
I was looking at :
http://manual.gromacs.org/online/getting_started.html#setup
Which mentions these files. Is this wrong ?
thanks,
Colin
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Chandan Choudhury
Sent: 12 Jun
Hi,
Search the mailing list. This problem and its solution has been repeatedly
discussed.
Erik
On 12 Jun 2013, at 10:31, Nikunj Maheshwari wrote:
> Dear all,
>
> I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> I am trying to use it for do_dssp command but get the foll
There are no such directory.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Jun 12, 2013 at 1:56 PM, colinbannister <
colin.bannis...@nottingham.ac.uk> wrote:
> Hope I'm not missing something obvious here - but I can't find the
> 'share/tutor' directory in my Gromacs 4.6 installat
Dear all,
I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
I am trying to use it for do_dssp command but get the following error each
time:
"Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
/dev/null 2> /dev/null
"
Is there any way to recti
Hope I'm not missing something obvious here - but I can't find the
'share/tutor' directory in my Gromacs 4.6 installation. Should it be there
?
thanks,
Colin
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Whether it would be that easy i will find it. I specified my own potential
(not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed
h(x) in my table 6th column.
On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul wrote:
>
>
> On 6/11/13 4:12 PM, Steven Neumann wrote:
>
>> Dear Grom
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