[gmx-users] Re:gmx-users Digest, Vol 84, Issue 81
fancy2012
fancy2012 at yeah.net
Sun Apr 10 15:25:58 CEST 2011
Dear Prof. Justin A. Lemkul,
Thanks very much for the website you supplied. It is very useful to me! Thank you again!
--
Best wishes,
Qinghua Liao
Ph.D student of Tianjin University, China
At 2011-04-10，gmx-users-request at gromacs.org wrote:
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>Today's Topics:
>
> 1. Re: NPT.mdp parameters NOTE (Peter C. Lai)
> 2. Re: converging value (Mark Abraham)
> 3. Re: Dangling bond error for dna (Justin A. Lemkul)
> 4. probelm of using amber force field (fancy2012)
> 5. Re: probelm of using amber force field (Justin A. Lemkul)
> 6. Re: converging value (mohsen ramezanpour)
> 7. Re: converging value (Mark Abraham)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Sun, 10 Apr 2011 05:02:10 -0500
>From: "Peter C. Lai" <pcl at uab.edu>
>Subject: Re: [gmx-users] NPT.mdp parameters NOTE
>To: mohsen ramezanpour <ramezanpour.mohsen at gmail.com>
>Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <20110410100210.GI54289 at cesium.hyperfine.info>
>Content-Type: text/plain; charset="us-ascii"
>
>He told me you can use up to 0.5 in an off-list email and in fact, does so
>in the KALP-15 in DPPC example...
>
>On 2011-04-10 02:54:15AM -0500, mohsen ramezanpour wrote:
>> Dear Dr.Justin
>>
>> As you have noticed in your tutorials,It is better to use Nose-Hoover for tempreture in the NPT.mdp file.
>> You have used tau-t = 0.1 in most of your md.mdp files for generating npt ensemble.
>>
>> When I use a npt file with these settings,there is a Note as following:
>> sorry,i can't remember the exact messge but :it says it is better to use a tau_t 20 times of another quantity,
>> in my work the quantity=0.01
>>
>> When I made tau_t=0.2 there was not any Note!
>>
>> Can I ignore this Note?Is it safe continuing with the same tau_t=0.1 as you used?
>>
>
>> --
>> 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!
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>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>--
>===============================================================
>Peter C. Lai | University of Alabama-Birmingham
>Programmer/Analyst | BEC 257
>Genetics, Div. of Research | 1150 10th Avenue South
>pcl at uab.edu | Birmingham AL 35294-4461
>(205) 690-0808 |
>===============================================================
>
>
>
>------------------------------
>
>Message: 2
>Date: Sun, 10 Apr 2011 20:39:25 +1000
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] converging value
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4DA188DD.7090804 at anu.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>On 10/04/2011 6:48 PM, mohsen ramezanpour wrote:
>> Dear All
>>
>> How can I determine the converged value of a simulation?
>> Because the pressure has big oscilations around it's converging value
>> but it is difficult to determine that value.
>
>Longer simulations on bigger systems.
>
>Mark
>
>
>------------------------------
>
>Message: 3
>Date: Sun, 10 Apr 2011 07:17:59 -0400
>From: "Justin A. Lemkul" <jalemkul at vt.edu>
>Subject: Re: [gmx-users] Dangling bond error for dna
>To: "Gromacs Users' List" <gmx-users at gromacs.org>
>Message-ID: <4DA191E7.3030707 at vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>majid hasan wrote:
>> Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted
>> below. Output of pdb2gmx is attached.
>>
>
>You have numerous problems with this .pdb file:
>
>1. All residues are listed as being the 3' end form. Your chain should start
>with a 5' end, include the "middle" residues, and end with a 3' form.
>
>2. 5' ends do not have phosphate on them, per force field convention.
>
>3. You have various incorrect atoms, and some incorrect atom names.
>
>Please refer to the dna.rtp file for your chosen force field to understand its
>expectations. Then you will need to manually fix your .pdb file by renaming,
>replacing, or removing whatever is in conflict.
>
>-Justin
>
>--
>========================================
>
>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: Sun, 10 Apr 2011 18:55:15 +0800 (CST)
>From: fancy2012 <fancy2012 at yeah.net>
>Subject: [gmx-users] probelm of using amber force field
>To: gmx-users <gmx-users at gromacs.org>
>Message-ID: <3ec402b.63dd.12f3f0d1e61.Coremail.fancy2012 at yeah.net>
>Content-Type: text/plain; charset="gbk"
>
>Dear GMX users,
>
>I have a question about running MD simulation using amber force field. It is easy to prepare the top and gro files of protein with amber force field, but how should I prepare the itp and gro files of small molecules with GAFF force field? I know the program ANTECHAMBER and tleap can generate the some molecule's topology and coordinate. Could someone give me some hints? Thanks very much in advance!
>
>--
>
>
>Best wishes,
>
>Qinghua Liao
>
>Ph.D student of Tianjin University, China
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>------------------------------
>
>Message: 5
>Date: Sun, 10 Apr 2011 07:32:13 -0400
>From: "Justin A. Lemkul" <jalemkul at vt.edu>
>Subject: Re: [gmx-users] probelm of using amber force field
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4DA1953D.7060006 at vt.edu>
>Content-Type: text/plain; charset=x-gbk; format=flowed
>
>
>
>fancy2012 wrote:
>> Dear GMX users,
>>
>> I have a question about running MD simulation using amber force
>> field. It is easy to prepare the top and gro files of protein with amber
>> force field, but how should I prepare the itp and gro files of small
>> molecules with GAFF force field? I know the program ANTECHAMBER and
>> tleap can generate the some molecule's topology and coordinate. Could
>> someone give me some hints? Thanks very much in advance!
>
>http://code.google.com/p/acpype/ is one common approach.
>
>-Justin
>
>>
>> --
>>
>> _Best wishes,_
>>
>> _Qinghua Liao_
>>
>> _Ph.D student of Tianjin University, China_
>>
>
>--
>========================================
>
>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: 6
>Date: Sun, 10 Apr 2011 16:11:28 +0430
>From: mohsen ramezanpour <ramezanpour.mohsen at gmail.com>
>Subject: Re: [gmx-users] converging value
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <BANLkTimNexPd1MujGF4b9zjAi4_RM_MpUw at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Dear Dr.Mark
>
>thank you for your attention
>How long is enough?
>for example I have run 200 ps for making npt(p=1 bar) for my system (300
>nm^3)
>But the pressure is oscilating so much,and I can't be sure if it has
>converged or not!
>of course its average is approximately 5 bar (at the end of log file)
>
>Do you have any idea?
>I know it is not any problem if a quantity is oscilating around it's
>converged value.
>
>thanks in advance for your reply
>
>On Sun, Apr 10, 2011 at 3:09 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>> On 10/04/2011 6:48 PM, mohsen ramezanpour wrote:
>>
>>> Dear All
>>>
>>> How can I determine the converged value of a simulation?
>>> Because the pressure has big oscilations around it's converging value but
>>> it is difficult to determine that value.
>>>
>>
>> Longer simulations on bigger systems.
>>
>> Mark
>> --
>> 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
>>
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>------------------------------
>
>Message: 7
>Date: Sun, 10 Apr 2011 21:57:12 +1000
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] converging value
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4DA19B18.2030501 at anu.edu.au>
>Content-Type: text/plain; charset="iso-8859-1"
>
>On 10/04/2011 9:41 PM, mohsen ramezanpour wrote:
>> Dear Dr.Mark
>>
>> thank you for your attention
>> How long is enough?
>
>For example, when the size of error estimate reported by g_energy is
>smaller than the quantity you are trying to observe. That might take
>many nanoseconds in the case of observables based on fluctuations of
>atomic positions. There've been lots of mailing list threads on this topic.
>
>Mark
>
>> for example I have run 200 ps for making npt(p=1 bar) for my system
>> (300 nm^3)
>> But the pressure is oscilating so much,and I can't be sure if it has
>> converged or not!
>> of course its average is approximately 5 bar (at the end of log file)
>>
>> Do you have any idea?
>> I know it is not any problem if a quantity is oscilating around it's
>> converged value.
>>
>> thanks in advance for your reply
>>
>> On Sun, Apr 10, 2011 at 3:09 PM, Mark Abraham <Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>
>> On 10/04/2011 6:48 PM, mohsen ramezanpour wrote:
>>
>> Dear All
>>
>> How can I determine the converged value of a simulation?
>> Because the pressure has big oscilations around it's
>> converging value but it is difficult to determine that value.
>>
>>
>> Longer simulations on bigger systems.
>>
>> Mark
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto: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
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>
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>End of gmx-users Digest, Vol 84, Issue 81
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