[gmx-users] Re: gmx-users Digest, Vol 76, Issue 59
farideh zergani
farideh_zergani at yahoo.com
Mon Dec 27 16:43:24 CET 2010
________________________________
From: "gmx-users-request at gromacs.org" <gmx-users-request at gromacs.org>
To: gmx-users at gromacs.org
Sent: Thu, August 12, 2010 2:32:17 AM
Subject: gmx-users Digest, Vol 76, Issue 59
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Today's Topics:
1. g_rms question (udi)
2. mdrun : error (Nilesh Dhumal)
3. Re: mdrun : error (Justin A. Lemkul)
4. need help (Anamika Awasthi)
5. Re: need help (Mark Abraham)
6. Re: g_rms question (Tsjerk Wassenaar)
7. trying to install gromacs on linux single processor
(Anamika Awasthi)
----------------------------------------------------------------------
Message: 1
Date: Thu, 12 Aug 2010 00:39:03 +0300
From: udi <udi_zel at 012.net.il>
Subject: [gmx-users] g_rms question
To: gmx-users at gromacs.org
Message-ID: <000001cb399d$9e2dee10$da89ca30$@net.il>
Content-Type: text/plain; charset="us-ascii"
Hi gromacs users,
I'm simulating a protein that consists of 5 domains. I have calculated the
whole protein's backbone RMSD by entering '4' twice.
Now, I would like to calculate the contribution of every domain i.e. if the
whole protein's RMSD in the first frame is 1nm, then how is this 1nm
distributed between the 5 domains.
I have created 5 groups in the index file of the backbone of every domain
and calculated the RMSD by first entering '4' in order to fit the whole
backbone and entered the domains backbone groups in the second entry. (5
different calculations). The problem is that the values I get from the
domains do not add up to the whole backbone RMSD values!!! What am doing
wrong?
Thanks from advanced
Chears
Udi
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Message: 2
Date: Wed, 11 Aug 2010 20:43:05 -0400
From: "Nilesh Dhumal" <ndhumal at andrew.cmu.edu>
Subject: [gmx-users] mdrun : error
To: gmx-users at gromacs.org
Message-ID:
<9bfc32c21b990b64977354fe7b803a7c.squirrel at webmail.andrew.cmu.edu>
Content-Type: text/plain;charset=iso-8859-1
Hello,
I am trying to do equilibration for my system (solvent + solute). I am
geting the following error. If I run solvent and solute molecules
separately, its run well. For mixture I am getting following error.
What this error means.
Fatal error:
1 of the 22334 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
NIlesh
------------------------------
Message: 3
Date: Wed, 11 Aug 2010 20:48:52 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] mdrun : error
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4C6344F4.8020009 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Nilesh Dhumal wrote:
> Hello,
> I am trying to do equilibration for my system (solvent + solute). I am
> geting the following error. If I run solvent and solute molecules
> separately, its run well. For mixture I am getting following error.
> What this error means.
>
> Fatal error:
> 1 of the 22334 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for
> pairs and tabulated bonds also see option -ddcheck
>
Search the list archive. This has been asked and answered several times, so
you'll likely find something useful. Also, take mdrun's advice and read about
the options it's telling you.
-Justin
> NIlesh
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 4
Date: Thu, 12 Aug 2010 12:09:50 +0530
From: Anamika Awasthi <aawasthi28 at gmail.com>
Subject: [gmx-users] need help
To: gmx-users at gromacs.org
Message-ID:
<AANLkTinqNjmg=z626T6XuAm4RvRP+zC01stohW2+7GuG at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear gromacs user,
I want to install gromacs new version on my linux system. can u all please
guide me,
Thanking u in advance
Anamika
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Message: 5
Date: Thu, 12 Aug 2010 16:51:53 +1000
From: Mark Abraham <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] need help
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <fbb4be4c2c0c2.4c6426a9 at anu.edu.au>
Content-Type: text/plain; charset="us-ascii"
----- Original Message -----
From: Anamika Awasthi <aawasthi28 at gmail.com>
Date: Thursday, August 12, 2010 16:41
Subject: [gmx-users] need help
To: gmx-users at gromacs.org
> Dear gromacs user,
>
> I want to install gromacs new version on my linux system. can u all please
>guide me,
The GROMACS installation guide can be found on the GROMACS webpage :-) There's a
ton of other useful information there, please be sure to search it and the rest
of the web before asking questions. You'll make much faster progress that way!
:-)
Mark
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Message: 6
Date: Thu, 12 Aug 2010 09:23:05 +0200
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] g_rms question
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<AANLkTi=8NnB+p_p+0S+ck-HVAuxE_a6VjDLZi4kMoJaO at mail.gmail.com>
Content-Type: text/plain; charset="windows-1252"
Hi Udi,
Square the numbers... It's Root Mean Square Deviation, right? But roots
don't add up like that.
Cheers,
Tsjerk
On Aug 12, 2010 12:02 AM, "udi" <udi_zel at 012.net.il> wrote:
Hi gromacs users,
I’m simulating a protein that consists of 5 domains. I have calculated the
whole protein’s backbone RMSD by entering ‘4’ twice.
Now, I would like to calculate the contribution of every domain i.e. if the
whole protein’s RMSD in the first frame is 1nm, then how is this 1nm
distributed between the 5 domains.
I have created 5 groups in the index file of the backbone of every domain
and calculated the RMSD by first entering ‘4’ in order to fit the whole
backbone and entered the domains backbone groups in the second entry. (5
different calculations). The problem is that the values I get from the
domains do not add up to the whole backbone RMSD values!!! What am doing
wrong?
Thanks from advanced
Chears
Udi
--
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Message: 7
Date: Thu, 12 Aug 2010 15:01:31 +0530
From: Anamika Awasthi <aawasthi28 at gmail.com>
Subject: [gmx-users] trying to install gromacs on linux single
processor
To: gmx-users at gromacs.org
Message-ID:
<AANLkTikpAN3JbMSSU67WPRoo0zntCKrpgvBrD51YF+By at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
hello all,
I am trying to install new version of gromacs on linux single processor,
getting this error
./configure --enable-threads --enable-float
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... configure: error: newly
created file is older than distributed files!
Check your system clock
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