Hi Mark,
What would be the difference between the shared lib and static lib?
Cheers,
Acoot
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Wednesday, 21 March 2012 2:38 PM
Subject: [gmx-users] resolution of cygwin installation issues
H
On 21/03/2012 6:44 PM, Acoot Brett wrote:
Hi Mark,
What would be the difference between the shared lib and static lib?
Google, or the top of the installation instructions, will tell you all
about that.
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman
Hi Berk,
Thank you for your help, after a short test, it seems to work perfect.
All the best
Tom
On 03/20/2012 10:11 AM, gmx-users-requ...@gromacs.org wrote:
Date: Tue, 20 Mar 2012 10:03:33 +0100
From: Berk Hess
Subject: RE: [gmx-users] Re: RE: problem with g_bar
To: Discussion list for GROMAC
Hello Florian,
I remembered a discussion with the same problem considering parameters
of Mg2+, here is the link:
http://comments.gmane.org/gmane.science.biology.gromacs.user/45437
The file given here
http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
mentions as source of the force
On Wed, 2012-03-21 at 09:13 +0100, Kathleen Kirchner wrote:
> Hello Florian,
>
> I remembered a discussion with the same problem considering parameters
> of Mg2+, here is the link:
>
> http://comments.gmane.org/gmane.science.biology.gromacs.user/45437
>
> The file given here
>
> http://dasher
Dear Gromacs users,
I am working on a program that need topology parsing.
I am using the OPLSAA forcefield and I noticed that in ffbonded.itp file
belonging to this force field there are these strange lines:
[ dihedraltypes ]
; ijkl func coefficients
; Added DvdS for Quartz simu
francesco oteri wrote:
Dear Gromacs users,
I am working on a program that need topology parsing.
I am using the OPLSAA forcefield and I noticed that in ffbonded.itp file
belonging to this force field there are these strange lines:
[ dihedraltypes ]
; ijkl func coefficient
OK,
but for some AMBER dihedral the same goal has been obtained using an X for
i and l atoms,
like:
X FE SS X 9 0.000.0 4
Why the same approach wasn't used for OPLSAA?
Il giorno 21 marzo 2012 11:35, Justin A. Lemkul ha
scritto:
>
>
> francesco oteri wrote:
On 21/03/2012 10:17 PM, francesco oteri wrote:
OK,
but for some AMBER dihedral the same goal has been obtained using an X
for i and l atoms,
like:
X FE SS X 9 0.000.0 4
Why the same approach wasn't used for OPLSAA?
Assuming Justin's right, then either appr
hello sir,
initially i did dynamics for my protein with 3water molecules.. it
went correctly..
when i thought of reducing water i decreased my box size so that my sol
number is around 7.
when i go for energy minimisation i got its output.. but when i analysed
its potential energy its co
priya thiyagarajan wrote:
hello sir,
initially i did dynamics for my protein with 3water molecules.. it
went correctly..
when i thought of reducing water i decreased my box size so that my sol
number is around 7.
when i go for energy minimisation i got its output.. but when i a
On 21/03/2012 10:48 PM, priya thiyagarajan wrote:
hello sir,
initially i did dynamics for my protein with 3water molecules..
it went correctly..
when i thought of reducing water i decreased my box size so that my
sol number is around 7.
when i go for energy minimisation i got its
On 21/03/2012 10:53 PM, Mark Abraham wrote:
On 21/03/2012 10:48 PM, priya thiyagarajan wrote:
hello sir,
initially i did dynamics for my protein with 3water molecules..
it went correctly..
when i thought of reducing water i decreased my box size so that my
sol number is around 7.
priya thiyagarajan wrote:
hello sir,
Thanks for your kind reply..
after energy minimisation i got this
Steepest Descents converged to Fmax < 1000 in 572 steps
*Potential Energy = -4.0509822e+05*
Maximum force = 9.1364709e+02 on atom 1747
Norm of force = 3.4970905e+01
when i g
hello sir,
Thanks a lot for your reply...
now i am clear with my potential energy..
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don'
Dear All,
Can you give me some suggestions on installing Xmgrace under cygwin? In the
make step it shows
"checking for a Motif >= 1002 compatible API... no
configure: error: M*tif has not been found"
How about the figure software (JPEG, PNG, PDF, etc)?
Cheers,
Acoot--
gmx-users mailing l
On 21/03/2012 11:50 PM, Acoot Brett wrote:
Dear All,
Can you give me some suggestions on installing Xmgrace under cygwin?
In the make step it shows
"checking for a Motif >= 1002 compatible API... no
configure: error: M*tif has not been found"
How about the figure software (JPEG, PNG, PDF, etc)?
Dear gromacs user,
I noted a strange behavior in topology generation workflow.
I have a protein whose active site contains a Ni atom linked to 4 Cys.
I inserted the 4 bonds by specbonds.dat. When I run pdb2gmx, I have
inspected
the Linking messages and they fit with the expected topology, I mean
Dear GMX users,
We are running GMX in linux platform. Any help in running DSSP program
is greatfully appreciated.
with thanks
Dr.C.Karunakaran
***+
Dr.Karunakaran Chandran+
Biophysics Department +
Medical College of Wisconsin +
Milwauke
On 22/03/2012 1:46 AM, francesco oteri wrote:
Dear gromacs user,
I noted a strange behavior in topology generation workflow.
I have a protein whose active site contains a Ni atom linked to 4 Cys.
I inserted the 4 bonds by specbonds.dat. When I run pdb2gmx, I have
inspected
the Linking message
Hello,
Upon continuing a replica exchange MD simulation using the command
mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 1 -cpt
60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e
edrRemd_20ns.edr -stepout 2000
I get the following output:
**
Hi all
I am trying to relax the density of an alcohol system that I have just
set up, but after a certain period of time I get the following error
Fatal error:
The X-size of the box (6.800588) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (4) times the smallest
It is possible that the system is unstable/exploding due atoms being too close
to each other in the initial system.
Andreas
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Gavin Melaugh
Sent: 21 March 2012 15:45
To: Discussion l
Hi Mark,
these are the involved residues extracted by the .top (CSA and CSB are
cysteines with modified partial charges):
; residue 62 CSB rtp CSB q -0.5
1010NH1 62CSB N 1010 -0.47 14.007 ;
qtot 0.53
1011 H 62CSB HN 1011 0.31
Dear users,
I have two configuration as the following related to Neigborsearching,
Electrostatics and vdw options. I checked the literature:
Generally the rlist, rcoulomb and rvdw have used as the following.
rlist=1
rcoulomb=0.8
rvdw=1.4
*Is there much difference between the following two options
Hi,
I am trying to simulate a liquid (EMI-BF4) in a box with two walls, one at
z=0 and one at z=z_0. I am trying to create a new atom type to use as my
walls' atom type, so that I can manipulate the interaction between the atoms
of the liquid and the atoms of the wall. I am basing this idea on t
Andrew DeYoung wrote:
Hi,
I am trying to simulate a liquid (EMI-BF4) in a box with two walls, one at
z=0 and one at z=z_0. I am trying to create a new atom type to use as my
walls' atom type, so that I can manipulate the interaction between the atoms
of the liquid and the atoms of the wall.
Justin,
Thank you so much for your help! That was really helpful.
It seems that I simply append my [ nonbond_params ] section to the end of my
ffnonbonded.itp file. However, if I ONLY have this:
---
; ffnonbonded.itp
[ atomtypes ]
;type at.n masscharge ptype sig eps
; all of the li
Andrew DeYoung wrote:
Justin,
Thank you so much for your help! That was really helpful.
It seems that I simply append my [ nonbond_params ] section to the end of my
ffnonbonded.itp file. However, if I ONLY have this:
---
; ffnonbonded.itp
[ atomtypes ]
;type at.n masscharge ptype
Dear users,
*Berk Hess says:
[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units
Mon Jul 16 14:17:12 CEST 2007*
There are three options in Gromacs.
The option you want is rcoulomb < rlist and rvdw < rlist.
This works and gives the most accurate and also the most costly int
Hi Mark,
But when I do the following:
plot "potential.xvg" using 1:2 with lines according to what you introduced, it
gives "Segmentation fault (core dumped)".
Can you explain to me how to solve the problem?
Cheers,
Acoot
From: Mark Abraham
To: Disc
Hi Ahmet,
> Let's imagine a sphere(two concentric spheres):
> radius of the inside small sphere=rvdw
> radius of the big sphere=rcoulomb
> distance between two of our nested spheres:rlist
> is this approach correct?
No. I suggest you read section 4.6.3 (and probably also 4.6.2) in the
Gromacs Ma
Dear All,
When I do "xmgrace potential.xvg",it shows
"Can't open display
Failed initializing GUI, exiting".
Will you please explain to me how to solve the problem?
Cheers,
Acoot--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please s
On 22/03/2012 10:16 AM, Acoot Brett wrote:
Hi Mark,
But when I do the following:
plot "potential.xvg" using 1:2 with lines according to what you
introduced, it gives "Segmentation fault (core dumped)".
Can you explain to me how to solve the problem?
You haven't made anywhere near enough descr
On 22/03/2012 10:34 AM, Acoot Brett wrote:
Dear All,
When I do "xmgrace potential.xvg",it shows
"Can't open display
Failed initializing GUI, exiting".
Will you please explain to me how to solve the problem?
No, this is not a general helpdesk for computing problems, and not even
that for GROMAC
Dear All,
Will you please suggest on how to select force field for the specific
requirement from the 18 force fields of the pdb2gmx of the gromacs 4.5.5
version?
Cheers,
Acoot --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please s
Easiest way is to use the same one that someone has published, that is dealing
with the same molecules and properties that you are interested in.
Each FF has been developed with particular properties and type of molecules in
mind. So you need to ensure it will deal with the ones you are interes
Hi
A protein sits on the top of another protein (not docking). I then used
pdb2gmx command to generate the topology. Surprisingly, i got five files,
as given below: I think the two proteins are not connected each other. is
it possible to make it one posre and topol file.
Many thanks in advance
Dear All,
I find some pdb files downloaded from RCSB cannot be recognized by pdb2gmx at
all.
Is any server which can convert and RCSB pdb files to files readable by pdb2gmx?
Cheers,
Acoot--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
On Thu, Mar 22, 2012 at 11:54 AM, Spring buds wrote:
> Hi
>
> A protein sits on the top of another protein (not docking). I then used
> pdb2gmx command to generate the topology. Surprisingly, i got five files,
> as given below: I think the two proteins are not connected each other. is it
> possib
On 22/03/2012 2:54 PM, Spring buds wrote:
Hi
A protein sits on the top of another protein (not docking). I then
used pdb2gmx command to generate the topology. Surprisingly, i got
five files, as given below: I think the two proteins are not
connected each other. is it possible to make it one
On 22/03/2012 5:13 AM, francesco oteri wrote:
Hi Mark,
these are the involved residues extracted by the .top (CSA and CSB are
cysteines with modified partial charges):
; residue 62 CSB rtp CSB q -0.5
1010NH1 62CSB N 1010 -0.47 14.007
; qtot 0.53
1011
On 22/03/2012 2:36 AM, Kukol, Andreas wrote:
Hello,
Upon continuing a replica exchange MD simulation using the command
mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 1 -cpt
60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e
edrRemd_20ns.edr -stepou
Hi Acoot,
What do you mean with 'not at all'? What is the output of pdb2gmx? Did you
check what is in those pdb files?
Cheers,
Tsjerk
On Mar 22, 2012 5:06 AM, "Acoot Brett" wrote:
Dear All,
I find some pdb files downloaded from RCSB cannot be recognized by pdb2gmx
at all.
Is any server whic
44 matches
Mail list logo
