S. Alireza B wrote
> My concern is that at the end of my 0.5 ns NVT run the T is ~300K;
> however,
> at the first step of my NVE, when no forces has exerted on unfrozen
> molecules yet, the T appears to be ~185K!
Your explanation of this issue given in the first post sounds very
meaningful. From g
Hi,
Here's a bit more explanation, hopefully a bit more practical and give for
you and others a better view of what's going on under mdrun's hood.
thread-MPI, or in other contexts referred to as "thread_mpi" or abbreviated
as "tMPI", is functionally equivalent with the standard MPI you'd use on
Hi all,
Let me clarify one thing: I highly doubt that the *gcc version* upgrade is
what fixes your the issue, but rather the standard C++ library's version,
as you can see the undefined symbols refer to "GLIBCXX_3.4.15".
Of course, updating the compiler is a perfectly fine solution if you get
the
Hi Alexey,
Justin found my error - ooops - misspelled one of the filenames.
Thank you for your reply!
Valentina
On 23 Jan 2013, at 19:50, Alexey Shvetsov wrote:
> Hi!
>
> What files do you have in .ff directory?
>
> Do you have files
> ffbonded.itp ffnonbonded.itp forcefield.doc forcefi
Hi!
What files do you have in .ff directory?
Do you have files
ffbonded.itp ffnonbonded.itp forcefield.doc forcefield.itp
Forcefield doc should have ff description like
AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
В письме от 23 января 2013 18:42:43 пользо
Ooops, thank you very much!
Dyslexic people & computers are not a good combination!
Valentina
On 23 Jan 2013, at 19:03, Justin Lemkul wrote:
>
>
> On 1/23/13 1:50 PM, Valentina Erastova wrote:
>> Awesome. Thank you very much.
>> I will email you a zip.
>
> I found the problem:
>
>> at
On 1/23/13 1:50 PM, Valentina Erastova wrote:
Awesome. Thank you very much.
I will email you a zip.
I found the problem:
atomtypes.atp ffbonded.itpffnonbonded.itp forcefield.doc forfecield.itp
molecule.rtp
Your forcefield.itp is spelled wrong. As such, the force field directory
Awesome. Thank you very much.
I will email you a zip.
Kind regards,
Valentina
__
Dr Valentina Erastova
Postdoctoral Research Assistant
Department of Earth Sciences
Durham University
Editor-in-Chief,
Kaleidoscope
+44 786 131 6686
On 23 Jan 2013, at 18:47, Justin Lemkul
On 1/23/13 1:42 PM, Valentina Erastova wrote:
Thank you for your reply Justin,
it is 4.5.5 ( i haven't yet got to instal 4.6 yet)
i tried it on Mac and Linux.
Shall I attach the files, may be?
The mailing list does not accept attachments. If you provide a link to where I
can download t
Just a follow up.
I have also tried using g_x2top and I am getting the same error.
Kind regards,
Valentina
__
Dr Valentina Erastova
Postdoctoral Research Assistant
Department of Earth Sciences
Durham University
Editor-in-Chief,
Kaleidoscope
+44 786 131 6686
On 23 Jan
On 1/23/13 1:43 PM, Debashis Sahu wrote:
Dear user,
Now I am trying a dynamics of a simple molecule binding with
an halide in gas phase in normal cpmd without any interface of
gromacs-cpmd. But this MD is not running properly after 15 steps. The
If you are working directly with
Dear user,
Now I am trying a dynamics of a simple molecule binding with
an halide in gas phase in normal cpmd without any interface of
gromacs-cpmd. But this MD is not running properly after 15 steps. The
output of this MD is following type :
* simple molecular dynamics deltat=4au
*
Thank you for your reply Justin,
it is 4.5.5 ( i haven't yet got to instal 4.6 yet)
i tried it on Mac and Linux.
Shall I attach the files, may be?
I have earlier written another forcefield and it worked without problems.
Kind regards,
Valentina
__
Dr Valentina Eras
On 1/23/13 1:22 PM, Valentina Erastova wrote:
Dear all,
I am having a bit of problem with pdb2gmx, when using self written force field.
I have created ClayyFF.ff containing:
atomtypes.atp ffbonded.itpffnonbonded.itp forcefield.doc forfecield.itp
molecule.rtp
also I have residuetype
Dear all,
I am having a bit of problem with pdb2gmx, when using self written force field.
I have created ClayyFF.ff containing:
atomtypes.atp ffbonded.itpffnonbonded.itp forcefield.doc forfecield.itp
molecule.rtp
also I have residuetypes.dat, stored next to the ClayFF.ff directory.
On 1/23/13 1:14 PM, Shima Arasteh wrote:
What I see in xvg file is as below:
# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
#
# g_rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@title "RMSD"
@xaxis label "Time (ps)"
@yaxis label "RMSD (nm)"
@TYPE xy
@ su
What I see in xvg file is as below:
# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
#
# g_rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@ title "RMSD"
@ xaxis label "Time (ps)"
@ yaxis label "RMSD (nm)"
@TYPE xy
@ subtitle "Protein after lsq fit to Protein"
On 1/23/13 12:48 PM, Shima Arasteh wrote:
I want to find the structure with the lowest RMSD, so I think it does not make
different to set any of pdb files as the ref structure.
I made an attempt and got the RMSD regarding the first pdb file. The RMSD
relative to -1 for the ref structure, is w
I want to find the structure with the lowest RMSD, so I think it does not make
different to set any of pdb files as the ref structure.
I made an attempt and got the RMSD regarding the first pdb file. The RMSD
relative to -1 for the ref structure, is written in xvg file. Is my approach
logically
On 01/22/2013 06:02 PM, Christoph Junghans wrote:
Message: 5
Date: Tue, 22 Jan 2013 19:42:01 +0100
From: Szil?rd P?ll
Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
Debian
To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset=ISO-
I think what you really need is not Gromacs.
For example, you can use UCSF Chimera to get alignment and RMSD between two
PDBs.
dawei
On Wed, Jan 23, 2013 at 10:38 AM, Shima Arasteh wrote:
>
>
> Hi,
>
> Is it possible to get RMSD of 10 different pdb files by GROMACS?
> g_rms may help?
>
>
>
On 1/23/13 10:38 AM, Shima Arasteh wrote:
Hi,
Is it possible to get RMSD of 10 different pdb files by GROMACS?
Relative to what? Each other? Some universal reference?
g_rms may help?
That, or g_confrms, depending on what you're actually trying to measure.
-Justin
--
=
Hi,
Is it possible to get RMSD of 10 different pdb files by GROMACS?
g_rms may help?
Sincerely,
Shima
--
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 bef
Hi Steven
I'm running simulations on DNA structures using the amber99sb-ildn FF. I
had no problem generating .top and .gro files
I might be able to help if you are interested.
send me the PDB file.
Yocheved
On Sun, Jan 20, 2013 at 10:57 PM, Tom wrote:
> Dear Gromacs User
>
> I built DNA with t
24 matches
Mail list logo
