[gmx-users] Archaeal lipid packages for CHARMM36
Wainwright, Josh
joshua.wainwright.11 at ucl.ac.uk
Wed Aug 13 18:22:16 CEST 2014
The lipid I'd like to use is called DPhPG, or officially 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol.
:-)
Thanks,
Josh
________________________________________
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Today's Topics:
1. Re: Polymer not diffusing into membrane (Justin Lemkul)
2. Re: RMSD graph over time and g_cluster RMSD distribution seem
at odds with each other (ms)
3. Re: Polymer not diffusing into membrane (Alex s)
4. error about g_bar (Swapnil Kate)
----------------------------------------------------------------------
Message: 1
Date: Wed, 13 Aug 2014 10:21:42 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Polymer not diffusing into membrane
Message-ID: <53EB7476.2080404 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 8/12/14, 10:45 PM, Alex s wrote:
> http://www.mediafire.com/view/63k3pi3k3hahnu3/snapshots(2).docxhttp://www.mediafire.com/view/02dk2kwj6tec939/mdp.txt
> hope this helps
Note the massive change in your box along z. Something has gone terribly wrong
in the simulation. Is your unit cell properly filled with water? Do you notice
anything else bizarre going on?
-Justin
>
> Date: Tue, 12 Aug 2014 21:58:09 -0400
>> From: jalemkul at vt.edu
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Polymer not diffusing into membrane
>>
>>
>>
>> On 8/12/14, 9:50 PM, Alex s wrote:
>>> I think that may well be the case. The polymer would move freely towards and away from the bilayer in the Z direction but would never diffuse or get close enough to interact. I've just run a simulation placing the polymer in a tight space with a bilayer above and below it and theres barely any movement of the polymer along the Z axis, its seems that there's something 'repelling' it any time it gets close to the bilayer. I've attached a text version of my mdp file, I would like to attach snapshots of my system setup but it would exceed the 50 KB limit.
>>
>> Post images (and any other files, for that matter) to file-sharing services and
>> provide the links.
>>
>> -Justin
>>
>>> Thanks
>>> Alex
>>>
>>>> Date: Tue, 12 Aug 2014 17:15:25 -0400
>>>> From: jalemkul at vt.edu
>>>> To: gmx-users at gromacs.org
>>>> Subject: Re: [gmx-users] Polymer not diffusing into membrane
>>>>
>>>>
>>>>
>>>> On 8/12/14, 1:35 PM, Alex s wrote:
>>>>> I've run it for 200 ns which I think is long enough allow the polymer to diffuse.
>>>>>
>>>>
>>>> If, as you say, it "never interacts or diffuses," it suggests that you're
>>>> applying some sort of restraint. Without seeing .mdp files and some sort of
>>>> quantitative measure of what you're seeing, it's hard to comment further.
>>>> Images would also be helpful. It depends on the size of the system and the
>>>> initial distance, but I would think you'd need far less than 200 ns to see such
>>>> an interaction.
>>>>
>>>> -Justin
>>>>
>>>>>> Date: Tue, 12 Aug 2014 10:41:52 +0200
>>>>>> From: devicerandom at gmail.com
>>>>>> To: gmx-users at gromacs.org
>>>>>> Subject: Re: [gmx-users] Polymer not diffusing into membrane
>>>>>>
>>>>>> How long is your simulation? Are you sure it is long enough to see what you
>>>>>> want to see?
>>>>>> On 12 Aug 2014 07:15, "Alex s" <as1783 at hotmail.com> wrote:
>>>>>>
>>>>>>> Dear Gromacs users
>>>>>>> I'm not sure if this a question suitable for this forum but I would
>>>>>>> greatly appreciate it if you can help me in anyway regarding this issue.
>>>>>>> I've have a system made up of a lipid bilayer, water and a single chain
>>>>>>> polymer. My aim is to place the polymer just above the lipid bilayer in
>>>>>>> the water phase and let it diffuse into the bilayer. This polymer has been
>>>>>>> shown to interact with the lipid bilayer in previous studies us. The issue
>>>>>>> I'm having is that in my simulation the polymer stays in the water phase
>>>>>>> just hovering above the lipid membrane and never interacts or diffuses.
>>>>>>> I've tried simulating it in a number of different ways by varying the
>>>>>>> number of water molecules, changing box size or polymer position however I
>>>>>>> haven't had any success yet. The main steps in setting up my system is as
>>>>>>> follows:
>>>>>>> 1. Simulate the Lipid bilayer alone to equilibrate it. 2. Take the final
>>>>>>> box size of the lipid bilayer and use it to place the Polymer at specific
>>>>>>> point just above the lipid bilayer. 3. Perform energy minimization on the
>>>>>>> system4. Perform NVT and NPT5. Run the simulation
>>>>>>> Any advice would be helpful
>>>>>>> Regards
>>>>>>> Alex
>>>>>>> --
>>>>>>> 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.
>>>>>
>>>>>
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 601
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
>>>> --
>>>> 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.
>>>
>>>
>>>
>>>
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> 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.
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 2
Date: Wed, 13 Aug 2014 16:25:03 +0200
From: ms <devicerandom at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] RMSD graph over time and g_cluster RMSD
distribution seem at odds with each other
Message-ID: <53EB753F.5070209 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 8/13/14 4:17 PM, Justin Lemkul wrote:
>
>> Aha! This makes much more sense then, thanks!
>> Is there a Gromacs command to get the histogram of RMSD against a single
>> reference structure, then?
>>
>
> You can construct histograms of any time series with g_analyze -dist.
OK, I forgot that. Thanks a lot, problem solved!
Massimo
------------------------------
Message: 3
Date: Wed, 13 Aug 2014 15:45:58 +0100
From: Alex s <as1783 at hotmail.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Polymer not diffusing into membrane
Message-ID: <COL129-W445D04FC2F123D7532A6C8D0EB0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
I should've mentioned that the those snapshots are of different system set ups. The first snapshot is for a system I set up by doubling the size of lipid box and placing the polymer just above the membrane. The second snaphshot is for a another system where I left the lipid box size as it was after equilibration and placing the polymer above the membrane. The only strange thing that I notice is the polymer is being almost 'repelled' by the bilayer.
Also is there an easy way to automatically fill the empty spaces in the box with water? The way I do it is quite tedious where I have to manually edit water boxes and position them to fill the empty space in the system box.
ThanksAlex
> Date: Wed, 13 Aug 2014 10:21:42 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Polymer not diffusing into membrane
>
>
>
> On 8/12/14, 10:45 PM, Alex s wrote:
> > http://www.mediafire.com/view/63k3pi3k3hahnu3/snapshots(2).docxhttp://www.mediafire.com/view/02dk2kwj6tec939/mdp.txt
> > hope this helps
>
> Note the massive change in your box along z. Something has gone terribly wrong
> in the simulation. Is your unit cell properly filled with water? Do you notice
> anything else bizarre going on?
>
> -Justin
>
> >
> > Date: Tue, 12 Aug 2014 21:58:09 -0400
> >> From: jalemkul at vt.edu
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Polymer not diffusing into membrane
> >>
> >>
> >>
> >> On 8/12/14, 9:50 PM, Alex s wrote:
> >>> I think that may well be the case. The polymer would move freely towards and away from the bilayer in the Z direction but would never diffuse or get close enough to interact. I've just run a simulation placing the polymer in a tight space with a bilayer above and below it and theres barely any movement of the polymer along the Z axis, its seems that there's something 'repelling' it any time it gets close to the bilayer. I've attached a text version of my mdp file, I would like to attach snapshots of my system setup but it would exceed the 50 KB limit.
> >>
> >> Post images (and any other files, for that matter) to file-sharing services and
> >> provide the links.
> >>
> >> -Justin
> >>
> >>> Thanks
> >>> Alex
> >>>
> >>>> Date: Tue, 12 Aug 2014 17:15:25 -0400
> >>>> From: jalemkul at vt.edu
> >>>> To: gmx-users at gromacs.org
> >>>> Subject: Re: [gmx-users] Polymer not diffusing into membrane
> >>>>
> >>>>
> >>>>
> >>>> On 8/12/14, 1:35 PM, Alex s wrote:
> >>>>> I've run it for 200 ns which I think is long enough allow the polymer to diffuse.
> >>>>>
> >>>>
> >>>> If, as you say, it "never interacts or diffuses," it suggests that you're
> >>>> applying some sort of restraint. Without seeing .mdp files and some sort of
> >>>> quantitative measure of what you're seeing, it's hard to comment further.
> >>>> Images would also be helpful. It depends on the size of the system and the
> >>>> initial distance, but I would think you'd need far less than 200 ns to see such
> >>>> an interaction.
> >>>>
> >>>> -Justin
> >>>>
> >>>>>> Date: Tue, 12 Aug 2014 10:41:52 +0200
> >>>>>> From: devicerandom at gmail.com
> >>>>>> To: gmx-users at gromacs.org
> >>>>>> Subject: Re: [gmx-users] Polymer not diffusing into membrane
> >>>>>>
> >>>>>> How long is your simulation? Are you sure it is long enough to see what you
> >>>>>> want to see?
> >>>>>> On 12 Aug 2014 07:15, "Alex s" <as1783 at hotmail.com> wrote:
> >>>>>>
> >>>>>>> Dear Gromacs users
> >>>>>>> I'm not sure if this a question suitable for this forum but I would
> >>>>>>> greatly appreciate it if you can help me in anyway regarding this issue.
> >>>>>>> I've have a system made up of a lipid bilayer, water and a single chain
> >>>>>>> polymer. My aim is to place the polymer just above the lipid bilayer in
> >>>>>>> the water phase and let it diffuse into the bilayer. This polymer has been
> >>>>>>> shown to interact with the lipid bilayer in previous studies us. The issue
> >>>>>>> I'm having is that in my simulation the polymer stays in the water phase
> >>>>>>> just hovering above the lipid membrane and never interacts or diffuses.
> >>>>>>> I've tried simulating it in a number of different ways by varying the
> >>>>>>> number of water molecules, changing box size or polymer position however I
> >>>>>>> haven't had any success yet. The main steps in setting up my system is as
> >>>>>>> follows:
> >>>>>>> 1. Simulate the Lipid bilayer alone to equilibrate it. 2. Take the final
> >>>>>>> box size of the lipid bilayer and use it to place the Polymer at specific
> >>>>>>> point just above the lipid bilayer. 3. Perform energy minimization on the
> >>>>>>> system4. Perform NVT and NPT5. Run the simulation
> >>>>>>> Any advice would be helpful
> >>>>>>> Regards
> >>>>>>> Alex
> >>>>>>> --
> >>>>>>> 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.
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>> ==================================================
> >>>>
> >>>> Justin A. Lemkul, Ph.D.
> >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>>
> >>>> Department of Pharmaceutical Sciences
> >>>> School of Pharmacy
> >>>> Health Sciences Facility II, Room 601
> >>>> University of Maryland, Baltimore
> >>>> 20 Penn St.
> >>>> Baltimore, MD 21201
> >>>>
> >>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>>> http://mackerell.umaryland.edu/~jalemkul
> >>>>
> >>>> ==================================================
> >>>> --
> >>>> 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.
> >>>
> >>>
> >>>
> >>>
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >> --
> >> 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.
> >
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> 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: 4
Date: Wed, 13 Aug 2014 23:19:08 +0800
From: Swapnil Kate <kate_swapnil at yahoo.com>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] error about g_bar
Message-ID:
<1407943148.52463.YahooMailNeo at web192501.mail.sg3.yahoo.com>
Content-Type: text/plain; charset=utf-8
hello,
I am trying to generate free energy of solvation using g_bar gromacs tool,
i have carried out all steps given in manual for solvation energy, but when i am trying to use g_bar command it shows 'nothing to calculate'.
what can be the possible errors because i am not getting correct values?
------------------------------
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