[gmx-users] RE:Stopping protein jumping inside box?
라지브간디
rajiv at kaist.ac.kr
Thu Feb 14 17:54:28 CET 2013
I have tried -pbc nojump, and other options given in that link but still my protein gets jumped! Plz guide me, how to stop this ?
--------------------- orig.Message ---------------------
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Today's Topics:
1. scattering vector analysis (Rajalakshmi.C)
2. RE: Stopping protein jumping inside box? (vivek modi)
3. Resuming of the trajectory calculation (James Starlight)
4. Re: Whether CHARMM force field in GROMACS is different from
that in CHARMM commercial package (David van der Spoel)
5. Re: Resuming of the trajectory calculation (Felipe Pineda, PhD)
6. Re: Resuming of the trajectory calculation (James Starlight)
7. Re: Resuming of the trajectory calculation (Felipe Pineda, PhD)
8. Number of interactions per residue (Kavyashree M)
----------------------------------------------------------------------
Message: 1
Date: Thu, 14 Feb 2013 12:00:26 +0530
From: "Rajalakshmi.C" <ch11d029 at smail.iitm.ac.in>
Subject: [gmx-users] scattering vector analysis
To: gmx-users at gromacs.org
Message-ID: <20130214062054.M45504 at smail.iitm.ac.in>
Content-Type: text/plain; charset=utf-8
hi all,
i have done scattering function analysis using g_rdf command for
polymer-solvent system. i got the plot of scattering vector q(1/nm) vs
intensity .now i want to convert the scattering vector (q) value in to
distance i.e. 'd' the fundamental polymer books have the relation for light
scattering, that relation is lamda= 2*d*sin(theta). this theta value can be
obtained from q.can anybody tell, what type of scattering gromacs use to
calculate q . and what is the relation to convert scattering vector q to
distance d for that particular scattering type which gromacs using
thanks in advance.
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Open WebMail Project (http://openwebmail.org)
------------------------------
Message: 2
Date: Thu, 14 Feb 2013 12:19:15 +0530
From: vivek modi <modi.vivek2009 at gmail.com>
Subject: [gmx-users] RE: Stopping protein jumping inside box?
To: gmx-users at gromacs.org
Message-ID:
<CADiSEiBymb77Bej-yU3TaUjk_tcGYr6bz1fQTnL-=HRFD18YDA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
>
> Message: 1
> Date: Thu, 14 Feb 2013 14:13:03 +0900 (KST)
> From: ????? <rajiv at kaist.ac.kr>
> Subject: [gmx-users] RE: Stopping protein jumping inside box?
> To: gmx-users at gromacs.org, gmx-users-request at gromacs.org
> Message-ID: <511c745f3fe9_ at _imoxion.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear gmx,
>
> I've used -pbc nojump options but still the protein goes all around the box within 4ns. Any specific command to avoid this ? It's a myoglobin protein!
Try this command.
http://www.mail-archive.com/gmx-users@gromacs.org/msg13353.html
Regards,
-Vivek
> --------------------- orig.Message ---------------------
> >From : gmx-users-request at gromacs.org
> To : gmx-users at gromacs.org
> Sent date : 2013-02-14 07:24
> Subject : gmx-users Digest, Vol 106, Issue 69
> Send gmx-users mailing list submissions to
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> Today's Topics:
>
> 1. Stopping protein jumping inside box (?????)
> 2. Re: Stopping protein jumping inside box (Naga Sundar)
> 3. Re: Stopping protein jumping inside box (Justin Lemkul)
> 4. RE: on the ussage of SD1 integrator (Berk Hess)
> 5. Chandler autcorrelation function fitting (KARAKAS Esra)
> 6. Bond potential of atom groups (Steven Neumann)
> 7. Join my network on LinkedIn (Gideon Lapidoth via LinkedIn)
> 8. GROMOS54A8 parameters in GROMACS format (ABEL Stephane 175950)
> 9. Re: different springs - WHAM (Steven Neumann)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 13 Feb 2013 22:29:05 +0900 (KST)
> From: ????? <rajiv at kaist.ac.kr>
> Subject: [gmx-users] Stopping protein jumping inside box
> To: gmx-users at gromacs.org
> Message-ID: <511b98243fa7_ at _imoxion.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear gmx users,
>
>
> I need to stop my protein jumping inside box. I have used -pbc mol -ur compact -center command too but still the protein gets moving from one place to other.
>
>
> Could you please suggest me how to make the protein to stop in one place ? Moreover, its protein with their ligand.
>
>
>
>
> Thnx.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 13 Feb 2013 05:47:07 -0800
> From: Naga Sundar <naga25sundar at gmail.com>
> Subject: Re: [gmx-users] Stopping protein jumping inside box
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CALobX4n_6hUoJhV-AEcjGj9UctvivV2H5U-+iZyVizmr0ECv6Q at mail.gmail.com>
> Content-Type: text/plain; charset=EUC-KR
>
> Hi
> Plz try -pbc nojump option...It may work
>
> On Wed, Feb 13, 2013 at 5:29 AM, ������������������������������ <rajiv at kaist.ac.kr> wrote:
>
>> Dear gmx users,
>>
>>
>> I need to stop my protein jumping inside box. I have used -pbc mol -ur
>> compact -center command too but still the protein gets moving from one
>> place to other.
>>
>>
>> Could you please suggest me how to make the protein to stop in one place ?
>> Moreover, its protein with their ligand.
>>
>>
>>
>>
>> Thnx.
>>
>>
>>
>> --
>> gmx-users mailing list gmx-users at 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't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Regards
> N.NagaSundaram
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 13 Feb 2013 08:50:04 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Stopping protein jumping inside box
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <511B9A0C.9 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> On 2/13/13 8:47 AM, Naga Sundar wrote:
>> Hi
>> Plz try -pbc nojump option...It may work
>>
>
> Several iterations of trjconv are often needed to achieve the desired
> representation. Indeed, the first step to removing jumps should be -pbc
> nojump...which removes jumps ;)
>
> -Justin
>
>> On Wed, Feb 13, 2013 at 5:29 AM, ��������������������������������������������� <rajiv at kaist.ac.kr> wrote:
>>
>>> Dear gmx users,
>>>
>>>
>>> I need to stop my protein jumping inside box. I have used -pbc mol -ur
>>> compact -center command too but still the protein gets moving from one
>>> place to other.
>>>
>>>
>>> Could you please suggest me how to make the protein to stop in one place ?
>>> Moreover, its protein with their ligand.
>>>
>>>
>>>
>>>
>>> Thnx.
>>>
>>>
>>>
>>> --
>>> gmx-users mailing list gmx-users at 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't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
------------------------------
Message: 3
Date: Thu, 14 Feb 2013 10:13:49 +0300
From: James Starlight <jmsstarlight at gmail.com>
Subject: [gmx-users] Resuming of the trajectory calculation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAALQopy8k6gpa_4jF5jW2Moo3=fcV47EcNvLc1g24ZjHMPprXQ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear Gromacs Users!
I have completed 100ns md trajectory.
I 'd like to go on that simulation adding extra 100 ns to the existing
trajectory (with appending of both trajectories in single file during
that simulation)
If I do it just via
mdrun -v -cpi md -deffnm md
the simulation have not gone on because the simulation time defined in
mdp file was over.
on contrary if I define new mdp file via grompt the second trajectory
save in the another file
Does it possible to continue simulation in the existing file?
James
------------------------------
Message: 4
Date: Thu, 14 Feb 2013 08:17:24 +0100
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Whether CHARMM force field in GROMACS is
different from that in CHARMM commercial package
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <511C8F84.1090008 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2013-02-14 07:02, fayaz wrote:
> Dear Gromacs Forum,
>
> I want to do RNA simulation using Gromacs. I have installed gromacs 4.5.5
> and i found Charmm force field present in it. Can I use this force field for
> my simulation. I am asking this because I heard that Charmm force field in
> Gromacs is incomplete and different from the one that is present in CHARMM
> software package. I think this conception is present with many of the
> gromacs users. Most of my friends are also not using Charmm force field that
> comes with gromacs. Please clear this doubt.
>
Please read the paper by Bjelkmar et al. about the implementation of the FF.
Rumors is not enough, but if there is concrete evidence that something
is incorrect a bug-report should be filed at http://redmine.gromacs.org.
Another question is whether Amber or Charmm is the better force field
for RNA. In my group we use Amber.
> Thanks in advance
>
> Fayaz
>
>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/Whether-CHARMM-force-field-in-GROMACS-is-different-from-that-in-CHARMM-commercial-package-tp5005524.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
------------------------------
Message: 5
Date: Thu, 14 Feb 2013 09:22:16 +0100
From: "Felipe Pineda, PhD" <luis.pinedadecastro at lnu.se>
Subject: Re: [gmx-users] Resuming of the trajectory calculation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <511C9EB8.4000700 at lnu.se>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
Very frequently it helps just to do some searches by your own and read
_carefully_ the documentation:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend
On 02/14/2013 08:13 AM, James Starlight wrote:
> Dear Gromacs Users!
>
> I have completed 100ns md trajectory.
>
> I 'd like to go on that simulation adding extra 100 ns to the existing
> trajectory (with appending of both trajectories in single file during
> that simulation)
>
> If I do it just via
>
> mdrun -v -cpi md -deffnm md
> the simulation have not gone on because the simulation time defined in
> mdp file was over.
>
>
> on contrary if I define new mdp file via grompt the second trajectory
> save in the another file
>
>
> Does it possible to continue simulation in the existing file?
>
> James
------------------------------
Message: 6
Date: Thu, 14 Feb 2013 12:11:33 +0300
From: James Starlight <jmsstarlight at gmail.com>
Subject: Re: [gmx-users] Resuming of the trajectory calculation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAALQopz_8FcRWKC55dyrHMwDjzhf5F4BaUWimtAhFFdVr0kT7g at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I've already tried to do it in accordance to that instructions!
firstly I've created new tpr file where I changed only duration of my simulation
grompp -f ./mdps/md_sd.mdp -n index -c old.tpr -o new.tpr
then I've launched mdrun
mdrun -v -s new.tpr -cpi old.cpi -deffnm old -append
where old is the name of all files from old simulation.
after this mdrun produced new set of all files and backuped (to the
#old) previous files. But I want to extend simuklation in my existing
files.
James
2013/2/14 Felipe Pineda, PhD <luis.pinedadecastro at lnu.se>:
> Very frequently it helps just to do some searches by your own and read
> _carefully_ the documentation:
>
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend
>
>
> On 02/14/2013 08:13 AM, James Starlight wrote:
>>
>> Dear Gromacs Users!
>>
>> I have completed 100ns md trajectory.
>>
>> I 'd like to go on that simulation adding extra 100 ns to the existing
>> trajectory (with appending of both trajectories in single file during
>> that simulation)
>>
>> If I do it just via
>>
>> mdrun -v -cpi md -deffnm md
>> the simulation have not gone on because the simulation time defined in
>> mdp file was over.
>>
>>
>> on contrary if I define new mdp file via grompt the second trajectory
>> save in the another file
>>
>>
>> Does it possible to continue simulation in the existing file?
>>
>> James
>
>
> --
> gmx-users mailing list gmx-users at 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't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
------------------------------
Message: 7
Date: Thu, 14 Feb 2013 10:17:57 +0100
From: "Felipe Pineda, PhD" <luis.pinedadecastro at lnu.se>
Subject: Re: [gmx-users] Resuming of the trajectory calculation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <511CABC5.9030207 at lnu.se>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
It's all about comprehending reading. If you look carefully at the
documentation again, you will find:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
What it's the right thing to do.
On 02/14/2013 10:11 AM, James Starlight wrote:
> I've already tried to do it in accordance to that instructions!
>
>
> firstly I've created new tpr file where I changed only duration of my simulation
> grompp -f ./mdps/md_sd.mdp -n index -c old.tpr -o new.tpr
>
> then I've launched mdrun
>
> mdrun -v -s new.tpr -cpi old.cpi -deffnm old -append
>
> where old is the name of all files from old simulation.
>
> after this mdrun produced new set of all files and backuped (to the
> #old) previous files. But I want to extend simuklation in my existing
> files.
>
> James
>
------------------------------
Message: 8
Date: Thu, 14 Feb 2013 15:12:13 +0530
From: Kavyashree M <hmkvsri at gmail.com>
Subject: [gmx-users] Number of interactions per residue
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAPLGqjp-KYWBdWWf2vJczawXncS7q3MUTyWGkBJwNwUoj0Xr9w at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear users,
How can I get the number of interactions of each residue
within a cut off as a function of time. just like g_saltbr writes
with the option -sep.
I tried using g_mdmat but it gives an average contact map.
Thank you
Kavya
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