[gmx-users] gmx insert-molecules
Shi Li
sli259 at g.uky.edu
Wed Jun 7 20:46:52 CEST 2017
> 在 2017年6月7日，13:31，gromacs.org_gmx-users-request at maillist.sys.kth.se 写道：
>
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: Simulate protein at subzero condition in aqueous buffer
> (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)
> 2. Re: Simulate protein at subzero condition in aqueous buffer
> (Jo?o Henriques)
> 3. gmx insert-molecules (Li, Shi)
> 4. Re: gmx insert-molecules (Justin Lemkul)
> 5. Re: Simulate protein at subzero condition in aqueous buffer
> (Jo?o Henriques)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 8 Jun 2017 01:07:40 +0800
> From: "=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=" <272699575 at qq.com>
> To: "=?ISO-8859-1?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?="
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Simulate protein at subzero condition in
> aqueous buffer
> Message-ID: <tencent_0991861F5B7B4403241DE643 at qq.com>
> Content-Type: text/plain; charset="ISO-8859-1"
>
> Dear Justin,
> Thank you very much. I will try the possible water models.
>
>
> Do you know if there are water models to resemble frozen state?
>
>
> Yours sincerely
> Cheng
>
>
>
>
> ------------------ Original ------------------
> From: "ZHANG Cheng";<272699575 at qq.com>;
> Date: Thu, Jun 8, 2017 00:50 AM
> To: "ZHANG Cheng"<272699575 at qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> Subject: Re: Simulate protein at subzero condition in aqueous buffer
>
>
>
> Dear Joao,
> Thank you for your help and the paper link.
>
>
> I was following Justin's tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
> On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models?
>
>
> I am trying to see if my protein will be denatured in cold condition.
>
>
> Yours sincerely
> Cheng
>
>
> ------------------ Original ------------------
> From: "ZHANG Cheng";<272699575 at qq.com>;
> Date: Wed, Jun 7, 2017 10:01 PM
> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> Cc: "ZHANG Cheng"<272699575 at qq.com>;
> Subject: Simulate protein at subzero condition in aqueous buffer
>
>
>
> Dear Gromacs,
> I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you.
>
>
> Yours sincerely
> Cheng
>
> ------------------------------
>
> Message: 2
> Date: Wed, 7 Jun 2017 19:15:58 +0200
> From: Jo?o Henriques <joao.m.a.henriques at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Simulate protein at subzero condition in
> aqueous buffer
> Message-ID:
> <CAHv45qPV=jte2gJx60r5BTrQZ0ZCBdb5bdmNSAypZ4TEt6BYvg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> ?Higher complexity water models such as TIP5P and so on are able to better
> reproduce bulk water properties (please check the paper I linked in my
> earlier email). However, these models require more computational effort
> (due to the increased number of interactions) and may not work well in
> conjunction with a protein (many protein force fields were developed to be
> used with specific water models)?. As Justin said, none of them gets
> everything right.
>
> /J
>
> On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699575 at qq.com> wrote:
>
>> Dear Justin,
>> Thank you very much. I will try the possible water models.
>>
>>
>> Do you know if there are water models to resemble frozen state?
>>
>>
>> Yours sincerely
>> Cheng
>>
>>
>>
>>
>> ------------------ Original ------------------
>> From: "ZHANG Cheng";<272699575 at qq.com>;
>> Date: Thu, Jun 8, 2017 00:50 AM
>> To: "ZHANG Cheng"<272699575 at qq.com>; "gromacs.org_gmx-users"<gromac
>> s.org_gmx-users at maillist.sys.kth.se>;
>>
>> Subject: Re: Simulate protein at subzero condition in aqueous buffer
>>
>>
>>
>> Dear Joao,
>> Thank you for your help and the paper link.
>>
>>
>> I was following Justin's tutorial
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>> gmx-tutorials/lysozyme/03_solvate.html
>> On that page, it says "spc216.gro as the solvent configuration for SPC,
>> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water)
>> after the solvation step. So I assume "spc216.gro" refer to all the
>> three-point water models?
>>
>>
>> I am trying to see if my protein will be denatured in cold condition.
>>
>>
>> Yours sincerely
>> Cheng
>>
>>
>> ------------------ Original ------------------
>> From: "ZHANG Cheng";<272699575 at qq.com>;
>> Date: Wed, Jun 7, 2017 10:01 PM
>> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>> Cc: "ZHANG Cheng"<272699575 at qq.com>;
>> Subject: Simulate protein at subzero condition in aqueous buffer
>>
>>
>>
>> Dear Gromacs,
>> I would like to simulate the protein at subzero condition in aqueous
>> buffer, to see if it becomes more stable than the elevated temperature
>> (e.g. 65 C). Can I ask what is the valid temperature range for water
>> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the
>> system as liquid state instead of frozen state? Thank you.
>>
>>
>> Yours sincerely
>> Cheng
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 7 Jun 2017 13:20:41 -0400
> From: "Li, Shi" <sli259 at g.uky.edu>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] gmx insert-molecules
> Message-ID:
> <CAC+hMcB5HEXt0iiS=dcMVZp++mf+7MNUfZimr=xJp6OfxnKDJA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear GMX users,
>
> I have a pure solvent system A with 100 molecules. Then I randomly removed
> 10 molecules out of the box, but keep the box size. Now I want to do a gmx
> insert-molecule to insert 10 molecule B into the system box. The problem is
> molecule B is slightly larger than molecule A. So in some cases, I couldn't
> insert the exact 10 molecules of B into the system. Is there a way to
> automatically adjust the size of the box according to the radius of
> molecule B, so that they can fit in? Or, is there a better solution to do
> this?
>
> Or, is there a way to ignore the overlapping of molecules? In that case,
> even the inserted molecule is overlapping with surrounding molecules, it
> can still be inserted in?
>
> Many thanks,
> Shi
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 7 Jun 2017 13:22:10 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gmx insert-molecules
> Message-ID: <90e50366-6813-1e41-e84a-b61061c28fe8 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 6/7/17 1:20 PM, Li, Shi wrote:
>> Dear GMX users,
>>
>> I have a pure solvent system A with 100 molecules. Then I randomly removed
>> 10 molecules out of the box, but keep the box size. Now I want to do a gmx
>> insert-molecule to insert 10 molecule B into the system box. The problem is
>> molecule B is slightly larger than molecule A. So in some cases, I couldn't
>> insert the exact 10 molecules of B into the system. Is there a way to
>> automatically adjust the size of the box according to the radius of
>> molecule B, so that they can fit in? Or, is there a better solution to do
>> this?
>>
>
> Insert 10 of molecule B into an empty box, then solvate with a pre-equilibrated
> box of molecule A. Works every time.
>
> -Justin
Thank you Justin,
In this case, I will need to apply a full equilibrium process (em, nvt, npt) to the new system, is that right?
I am trying to avoid the long step of equilibrium as I have many systems corresponding to different concentrations. I was thinking if I replace a small number of molecule A with molecule B (the system A is very large and pre-equilibriumed) then I only need to apply a short time-step of NPT in order to let the system expand or shrink. Then I can use the new system to continue replacing A with B to generate a new concentration. Is this practical?
The problem is when B is slightly larger than A, I can’t insert the same number of B into the system. Is there way to avoid the overlapping or force the molecule in?
Thanks,
Shi
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 7 Jun 2017 19:31:29 +0200
> From: Jo?o Henriques <joao.m.a.henriques at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Simulate protein at subzero condition in
> aqueous buffer
> Message-ID:
> <CAHv45qNELCjNbA5+Gox2CM3H4iUvp0TLqEjv5mpSxMQZs-5nxQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Just one more thing. If you're following Justin's tutorial, I guess you're
> using lysozyme. This protein will not deviate very much from it's crystal
> structure at 27?C, let alone at -40?C (*in the context of a molecular
> dynamics simulation**). I understand that it may be possible to
> experimentally unfold this protein reversibly using low temperature and
> high pressure, but this may be unfeasible to perform using a regular
> protein force field and water model. It will not behave as you expect.
>
> * I should add that this is a very stable protein and the disulfide bonds
> (which cannot be broken during the simulation) make it almost impossible to
> unfold it completely at any temperature using molecular dynamics.
>
> /J
>
>
>
> On Wed, Jun 7, 2017 at 7:15 PM, Jo?o Henriques <joao.m.a.henriques at gmail.com
>> wrote:
>
>> ?Higher complexity water models such as TIP5P and so on are able to better
>> reproduce bulk water properties (please check the paper I linked in my
>> earlier email). However, these models require more computational effort
>> (due to the increased number of interactions) and may not work well in
>> conjunction with a protein (many protein force fields were developed to be
>> used with specific water models)?. As Justin said, none of them gets
>> everything right.
>>
>> /J
>>
>> On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699575 at qq.com> wrote:
>>
>>> Dear Justin,
>>> Thank you very much. I will try the possible water models.
>>>
>>>
>>> Do you know if there are water models to resemble frozen state?
>>>
>>>
>>> Yours sincerely
>>> Cheng
>>>
>>>
>>>
>>>
>>> ------------------ Original ------------------
>>> From: "ZHANG Cheng";<272699575 at qq.com>;
>>> Date: Thu, Jun 8, 2017 00:50 AM
>>> To: "ZHANG Cheng"<272699575 at qq.com>; "gromacs.org_gmx-users"<gromac
>>> s.org_gmx-users at maillist.sys.kth.se>;
>>>
>>> Subject: Re: Simulate protein at subzero condition in aqueous buffer
>>>
>>>
>>>
>>> Dear Joao,
>>> Thank you for your help and the paper link.
>>>
>>>
>>> I was following Justin's tutorial
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>>> -tutorials/lysozyme/03_solvate.html
>>> On that page, it says "spc216.gro as the solvent configuration for SPC,
>>> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water)
>>> after the solvation step. So I assume "spc216.gro" refer to all the
>>> three-point water models?
>>>
>>>
>>> I am trying to see if my protein will be denatured in cold condition.
>>>
>>>
>>> Yours sincerely
>>> Cheng
>>>
>>>
>>> ------------------ Original ------------------
>>> From: "ZHANG Cheng";<272699575 at qq.com>;
>>> Date: Wed, Jun 7, 2017 10:01 PM
>>> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>>> Cc: "ZHANG Cheng"<272699575 at qq.com>;
>>> Subject: Simulate protein at subzero condition in aqueous buffer
>>>
>>>
>>>
>>> Dear Gromacs,
>>> I would like to simulate the protein at subzero condition in aqueous
>>> buffer, to see if it becomes more stable than the elevated temperature
>>> (e.g. 65 C). Can I ask what is the valid temperature range for water
>>> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the
>>> system as liquid state instead of frozen state? Thank you.
>>>
>>>
>>> Yours sincerely
>>> Cheng
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
>>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 158, Issue 44
> ******************************************************
More information about the gromacs.org_gmx-users
mailing list