[gmx-users] RE: Anisotropic pressure control

[Justin A. Lemkul]

Matteus Lindgren wrote:
> Thank you for the comment. 
> I understand your confusion. Yes, the volume of the box volume should
> fluctuate with pressure control but not on the large scale that I get. The
> box fluctuates and does not seem to settle on a certain volume. I have tried
> with the Berendsen algorithm as well but that run crashed. When I remove the
> frozen TiO2 surface the box volume does not at all fluctuate as much. It
> therefore seems to be some problem with the frozen atoms and pressure
> control. 
> 
> Any ideas about this?
> 

Does the simulation still crash under NVT conditions?  I know there has been a 
long-standing incompatibility of pressure coupling with frozen groups, although 
I believe that is the purpose of the new .mdp option "refcoord_scaling" - how 
are you setting this option?

-Justin

> Thanks
> Matteus
>   
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of gmx-users-request at gromacs.org
> Sent: den 1 mars 2010 01:18
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 71, Issue 1
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> Today's Topics:
> 
>    1. simulation settings (politr at fh.huji.ac.il)
>    2. Re: simulation settings (Mark Abraham)
>    3. Question about distance restraints,	energy minimization and
>       time averaging. (Arthur Roberts)
>    4. Re: Question about distance restraints,	energy minimization
>       and time averaging. (Erik Marklund)
>    5. NVE of water (Andrea)
>    6. RE: Anisotropic pressure control (Dallas B. Warren)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 28 Feb 2010 15:00:11 +0200
> From: politr at fh.huji.ac.il
> Subject: [gmx-users] simulation settings
> To: gmx-users at gromacs.org
> Message-ID: <20100228150011.61721j3pdrw2efog at webmail.huji.ac.il>
> Content-Type: text/plain;	charset=UTF-8;	DelSp="Yes";
> format="flowed"
> 
> Dear Gromacs users and developers,
> I want to perform simulation of peptide dissolved in water using NPT.  
> For constant temperature I use Berendsen temperature coupling. Do I  
> have to define tc-grps for 2 groups (protein and solvent) or I may use  
> tc-grps =System.
> What is the difference? The person who introduced gromacs to me uses
> tc-grps             =  Protein		Sol_Ions
> but he is not sure why it should be in this way if at all
> Can you, please elucidate this issue to me.
> Thank you a lot.
> Regina
> 
> ----------------------------------------------------------------
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> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 01 Mar 2010 00:50:42 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] simulation settings
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B8A74B2.3050206 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> On 1/03/2010 12:00 AM, politr at fh.huji.ac.il wrote:
>> Dear Gromacs users and developers,
>> I want to perform simulation of peptide dissolved in water using NPT.
>> For constant temperature I use Berendsen temperature coupling. Do I have
>> to define tc-grps for 2 groups (protein and solvent) or I may use
>> tc-grps =System.
>> What is the difference? The person who introduced gromacs to me uses
>> tc-grps = Protein Sol_Ions
>> but he is not sure why it should be in this way if at all
>> Can you, please elucidate this issue to me.
> 
> There's some quick advice here 
> http://www.gromacs.org/Documentation/Terminology/Thermostats, otherwise 
> consult some textbook material.
> 
> Mark
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Sun, 28 Feb 2010 10:25:24 -0800
> From: Arthur Roberts <aroberts99163 at yahoo.com>
> Subject: [gmx-users] Question about distance restraints,	energy
> 	minimization and time averaging.
> To: gmx users <gmx-users at gromacs.org>
> Message-ID: <9ED0AA2D-C946-40BC-B85B-844962C4D2D2 at yahoo.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
> 
> Hi, all,
> 
> This is probably a very simple question.  Does time averaging apply,
> when distance restraints are used during energy minimization (steepest
> descent or conjugate gradient)?  Your input would be greatly
> appreciated.
> 
> Art Roberts
> 
> Dr. Arthur Roberts, Ph.D.
> University of California, San Diego
> Skaggs School of Pharmacy and Pharmaceutical Sciences
> 9500 Gilman Drive #0703
> La Jolla, CA 92093-0703
> 
> email: aroberts99163 at yahoo.com
> cell: 206-850-7468
> skype=aroberts92122
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Sun, 28 Feb 2010 20:53:38 +0100
> From: Erik Marklund <erikm at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Question about distance restraints,	energy
> 	minimization and time averaging.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B8AC9C2.3030906 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi,
> 
> I'm not sure if I understand exactly what you meen, but since there's no 
> time propagation during energy minimization, time-averages don't make 
> much sense.
> 
> Erik
> 
> Arthur Roberts skrev:
>> Hi, all,
>>
>> This is probably a very simple question.  Does time averaging apply,
>> when distance restraints are used during energy minimization (steepest
>> descent or conjugate gradient)?  Your input would be greatly
>> appreciated.
>>
>> Art Roberts
>>
>> Dr. Arthur Roberts, Ph.D.
>> University of California, San Diego
>> Skaggs School of Pharmacy and Pharmaceutical Sciences
>> 9500 Gilman Drive #0703
>> La Jolla, CA 92093-0703
>>
>> email: aroberts99163 at yahoo.com
>> cell: 206-850-7468
>> skype=aroberts92122
>>
>>
>>
> 
> 

-- 
========================================

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

========================================