Hi,
Make sure you do specify the explicit names of the topology and structure
file. in the mannual they omit the suffix of the file.
for the purpose of rigourism - this is the line i'm using:
genion -pname Na+ -nname Cl- -o file_ionized.gro -conc 0.2 -p
topol.top
On Tue, Nov 17, 2009
Dear gmxuser
I want to compare a dimer covariance which was already run in 2 different
situation. The problem is that the scale of produced covariance (which
produced by -xpma) in 2 case is different e.g the scale for one of them
start from -0.18 to 0.05 and other -0.15 to 0.052. Is there any
poss
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul
Sent: Thu 19-11-2009 02:09
To: Gromacs Users' List
Subject: Re: SV: SV: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote:
>
>
> Sarah Witzke wrote:
>
>
>
>> ARRGH, I'm sorry, things went too
Hi,gmx users,
I want to set CNT infinite
in the system of CNT and water. I'm using GMX 4.1,so I have set pbc=xyz,
periodic_molecules=yes in mdp file.
I set the box size larger than CNT's length a C-C bond(half up and half
down).
If I don't do a EM, it will crumble. But if I do it,it can't satisfy
Sarah Witzke wrote:
-Original Message- From: gmx-users-boun...@gromacs.org on behalf of
Justin A. Lemkul Sent: Thu 19-11-2009 02:09 To: Gromacs Users' List Subject:
Re: SV: SV: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote:
Sarah Witzke wrote:
ARRGH, I'm sorry, things w
Cun Zhang wrote:
Hi,gmx users,
I want to set CNT infinite in the system of CNT and water. I'm using
GMX 4.1,so I have set pbc=xyz, periodic_molecules=yes in mdp file.
Not possible, Gromacs 4.1 hasn't been released :) If you're using version
4.0.1, you shouldn't, because it has a nasty bug
Hi Morteza,
Your question suggests a lack of understanding of the principles (not
principals) of covariance analysis. It is probably best to read a bit
more on the background of this technique, until you realize what it
is, what it can do, and what it can't. There are a number of
discussions archi
What are the main differences between the force fields used in gromacs? In
which scenarios are each force field better to use?
Chanel
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
Smith, Chanel Chonda wrote:
What are the main differences between the force fields used in gromacs? In
which scenarios are each force field better to use?
I think this question is best addressed by a thorough examination of the
literature and the various textbooks that exist regarding sim
Dear Tsjerk
Thanks for your help and reply. I thing my question was not clear.
I want to compare 2 covariance map. but in one map the red colour shows e.g
1 nm^2 fluctuation and in other map the red colour shows e.g 0.5 nm^2
fluctuation. I wanted that both map be in the same scale of colour
inten
Hi,
Is there any gromacs utility to calculate the hydrated radius of ions?
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search th
Dear all,
I'm trying to evaluate the number of H-bonds in a 150 alcohol (TraPPE)
+ 57 water (SPC/E) molecules mixture.
>From rdf analysis I can observe that the most prominent peak is
related to OW-OW group, followed by OW-OH group and finally OH-OH
group.
OW = water oxygen
OH = alcohol oxygen.
Justin, thanks for your reply. By the way, your GMX tutorials is great!
I post the gro file and mdp file at the end.
On Thu, Nov 19, 2009 at 10:09 PM, Justin A. Lemkul wrote:
>
> Not possible, Gromacs 4.1 hasn't been released :) If you're using version
> 4.0.1, you shouldn't, because it has a
Hi,
how can I use different coulomb 1-4 interactions in the A and B state.
The Manual just says
[ pairs ] : LJ and Coulomb 1-4 interactions
but, I far as I could see, did not give an example how the coulomb 1-4
interaction can be explicitly given.
Thanks a lot for any help,
Jochen
--
--
Cun Zhang wrote:
I mean, I make the distance of the top ( or bottom ) C atoms in CNT and
the corresponding edge of the box equals the length of a C-C bond( about
0.142nm ).
OK, that sounds reasonable, but did you define the periodic bonds appropriately?
Your original question was that
Hi Morteza,
To me, your initial question seemed to relate to scaling/constraining
the covariances. But I also take most any opportunity to warn people
not to think too ligthly about PCA :) You can use xpm2ps to combine
the matrices and recolorize according to the range of the combined
set.
Hope i
Hi,
There are automatically different, since they are based on the A and B state
charges
and the A and B state atom types.
Berk
> Date: Thu, 19 Nov 2009 16:15:52 +0100
> From: joc...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: [gmx-users] FEP with bond formation, pair problem
>
> Hi
The selection of FF depends on what you study. Perhaps, none of them
will be useful for you. The existing ones differ at least by the
procedures if generation although many parameters are very close.
>
> What are the main differences between the force fields used in gromacs? In
> which scenarios
Berk Hess wrote:
Hi,
There are automatically different, since they are based on the A and B
state charges
and the A and B state atom types.
But the problem is more complicated:
Let's say there is a Butane radical C4H9. that you want to bond to
another butane radical to form octane (C8H18).
David van der Spoel wrote:
Berk Hess wrote:
Hi,
There are automatically different, since they are based on the A and
B state charges
and the A and B state atom types.
But the problem is more complicated:
Let's say there is a Butane radical C4H9. that you want to bond to
another butane rad
Hi Gerrit,
I would like to use 6-31G** for my QMMM-calculation. Since sulfur is
part of my QM system, I consider that a sensible thing to do.
Unfortunately, it is not implemented in Gromacs, so I tried to add
that bit myself.
Here's the point where I got stuck:
src/mdlib/qm_gaussian.c
ilona.bal...@bioquant.uni-heidelberg.de wrote:
Hi Gerrit,
I would like to use 6-31G** for my QMMM-calculation. Since sulfur is
part of my QM system, I consider that a sensible thing to do.
Unfortunately, it is not implemented in Gromacs, so I tried to add that
bit myself.
Here's the point
Dear all,
I'm running some simulations using Gromacs/CPMD but it doesn't continue
during QMCONTINUE file lecture. See below:
EXTERNAL ENERGY= 5.867019924829098E-002 AU
REAL TOTAL ENERGY = -97.3517503273190 AU
ATOM COORDINATESGRADIENTS (-FORCES)
1 C
g_rdf ?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a ha
Hello,
How do you check for bad contacts in a system that cannot be minimized?
Thanks,
Lum
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subsc
When you try to minimise, it will typically tell you the worst offending
atoms in your system. Which you can then check visually using VMD etc
and try and work out why it is an issue. Then you can adjust how the
system was set up to fix the issue.
Also, if you just look at the system visually
I must have asked this before but I'm trying find the answer again. If
I want to use the results from mdrun for another run following the
first time interval, what do I need to do?
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
--
gmx-users mailing listgmx-users@gromacs.or
Jack Shultz wrote:
I must have asked this before but I'm trying find the answer again. If
I want to use the results from mdrun for another run following the
first time interval, what do I need to do?
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
-Justin
--
=
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
Hi With the periodic boundary condition, all the recorded coordinates of the
atom are within the simulation box. To calculate the MSD, the movement of
the center mass of the molecules between this time step with the next time
step is calculated without considering the periodic boundary condition. B
Chih-Ying Lin wrote:
Hi With the periodic boundary condition, all the recorded coordinates of
the atom are within the simulation box. To calculate the MSD, the
movement of the center mass of the molecules between this time step with
the next time step is calculated without considering th
Hi, all,
I am newcomer of gmx, and I want to know how to make a porcupine plot after a
essential MD. I found it looks nicer than linear interpolations between two
extremes.
Thanks in advance!
Atonio--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-
AntonioLeung wrote:
Hi, all,
I am newcomer of gmx, and I want to know how to make a porcupine plot
after a essential MD. I found it looks nicer than linear interpolations
between two extremes.
Thanks in advance!
There are not tools in Gromacs to do such a thing, but a simple Google search
33 matches
Mail list logo