Re: [gmx-users] Deletion of Lipids During InflateGro?

[Justin Lemkul]

On 12/31/16 11:30 PM, Sanim Rahman wrote:

Thank you Justin,

Here are the commands I used:

*gmx_mpi genconf -f popc.gro -o popc_full.gro -nbox 2 1 1*

*perl inflategro.pl  popc_full.gro 4 POPC 1
popc_inflated.gro 5 area.dat*



There is no reason to run InflateGRO on a pure membrane.  You're just re-packing 
already equilibrated lipids.  I don't know if I can offer an explanation about 
your observations, but this is simply an unnecessary process and perhaps 
something weird is going on.


-Justin


The first command was used to extend the length of my bilayer and the
second was to inflate the structure. When I run the second command it reads
that there are 128 lipids in the structure. My popc.gro originally had 128
and after using the genconf command I doubled it to 256. I checked my
popc_full.gro file in VMD and opened the file in an open text editor to
ensure that it was 256 lipids.

I compared my popc_inflated.gro file to my popc.gro file inflated under the
same parameters. They were exactly the same. Thank you for your assistance.

Regards,
Sanim Rahman

On Fri, Dec 30, 2016 at 11:55 AM, Justin Lemkul  wrote:




On 12/29/16 10:32 PM, Sanim Rahman wrote:


Dear Gromacs Users,

I am working on building a lipid bilayer for my protein structure but I am
having difficulty using the InflateGRO script.

I am using a POPC bilayer and used the genconf command to extend the
length
of the bilayer so I would be able to go from having 128 to 256 lipids. The
POPC bilayer I have is already converged so I plan to inflate the bilayer
using InflateGRO, insert my protein in the center, and then converge to
the
appropriate lipid per area value with the script. My issue is that when I
inflate the bilayer the script reduces the bilayer back to 128 lipids.

I tried another approach by inflating my 128 lipid bilayer and then using
the genconf command to obtain 256 lipids. However, when converging my
bilayer, the lipids did not converge to the center of the entire system
but
the center of its own 128 lipid system, meaning that the bilayer split off
into two separate pieces.

Is there a way to have the script avoid reducing the number of lipids in
the system in my original method?



Lipids will always be deleted by InflateGRO because some will overlap with
the protein.  It won't delete 128 unless your protein really does occupy
50% of the membrane area.  Be sure you're using the right files as input.
If you need further help, please copy and paste your exact sequence of
commands so we can see what you're doing.

-Justin

--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Deletion of Lipids During InflateGro?

[Sanim Rahman]

Thank you Justin,

Here are the commands I used:

*gmx_mpi genconf -f popc.gro -o popc_full.gro -nbox 2 1 1*

*perl inflategro.pl  popc_full.gro 4 POPC 1
popc_inflated.gro 5 area.dat*

The first command was used to extend the length of my bilayer and the
second was to inflate the structure. When I run the second command it reads
that there are 128 lipids in the structure. My popc.gro originally had 128
and after using the genconf command I doubled it to 256. I checked my
popc_full.gro file in VMD and opened the file in an open text editor to
ensure that it was 256 lipids.

I compared my popc_inflated.gro file to my popc.gro file inflated under the
same parameters. They were exactly the same. Thank you for your assistance.

Regards,
Sanim Rahman

On Fri, Dec 30, 2016 at 11:55 AM, Justin Lemkul  wrote:

>
>
> On 12/29/16 10:32 PM, Sanim Rahman wrote:
>
>> Dear Gromacs Users,
>>
>> I am working on building a lipid bilayer for my protein structure but I am
>> having difficulty using the InflateGRO script.
>>
>> I am using a POPC bilayer and used the genconf command to extend the
>> length
>> of the bilayer so I would be able to go from having 128 to 256 lipids. The
>> POPC bilayer I have is already converged so I plan to inflate the bilayer
>> using InflateGRO, insert my protein in the center, and then converge to
>> the
>> appropriate lipid per area value with the script. My issue is that when I
>> inflate the bilayer the script reduces the bilayer back to 128 lipids.
>>
>> I tried another approach by inflating my 128 lipid bilayer and then using
>> the genconf command to obtain 256 lipids. However, when converging my
>> bilayer, the lipids did not converge to the center of the entire system
>> but
>> the center of its own 128 lipid system, meaning that the bilayer split off
>> into two separate pieces.
>>
>> Is there a way to have the script avoid reducing the number of lipids in
>> the system in my original method?
>>
>>
> Lipids will always be deleted by InflateGRO because some will overlap with
> the protein.  It won't delete 128 unless your protein really does occupy
> 50% of the membrane area.  Be sure you're using the right files as input.
> If you need further help, please copy and paste your exact sequence of
> commands so we can see what you're doing.
>
> -Justin
>
> --
> ==
>
> 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
>
> jalem...@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-requ...@gromacs.org.
>
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Re: [gmx-users] Deletion of Lipids During InflateGro?

[Justin Lemkul]

On 12/29/16 10:32 PM, Sanim Rahman wrote:

Dear Gromacs Users,

I am working on building a lipid bilayer for my protein structure but I am
having difficulty using the InflateGRO script.

I am using a POPC bilayer and used the genconf command to extend the length
of the bilayer so I would be able to go from having 128 to 256 lipids. The
POPC bilayer I have is already converged so I plan to inflate the bilayer
using InflateGRO, insert my protein in the center, and then converge to the
appropriate lipid per area value with the script. My issue is that when I
inflate the bilayer the script reduces the bilayer back to 128 lipids.

I tried another approach by inflating my 128 lipid bilayer and then using
the genconf command to obtain 256 lipids. However, when converging my
bilayer, the lipids did not converge to the center of the entire system but
the center of its own 128 lipid system, meaning that the bilayer split off
into two separate pieces.

Is there a way to have the script avoid reducing the number of lipids in
the system in my original method?



Lipids will always be deleted by InflateGRO because some will overlap with the 
protein.  It won't delete 128 unless your protein really does occupy 50% of the 
membrane area.  Be sure you're using the right files as input.  If you need 
further help, please copy and paste your exact sequence of commands so we can 
see what you're doing.


-Justin

--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] Deletion of Lipids During InflateGro?

[Sanim Rahman]

Dear Gromacs Users,

I am working on building a lipid bilayer for my protein structure but I am
having difficulty using the InflateGRO script.

I am using a POPC bilayer and used the genconf command to extend the length
of the bilayer so I would be able to go from having 128 to 256 lipids. The
POPC bilayer I have is already converged so I plan to inflate the bilayer
using InflateGRO, insert my protein in the center, and then converge to the
appropriate lipid per area value with the script. My issue is that when I
inflate the bilayer the script reduces the bilayer back to 128 lipids.

I tried another approach by inflating my 128 lipid bilayer and then using
the genconf command to obtain 256 lipids. However, when converging my
bilayer, the lipids did not converge to the center of the entire system but
the center of its own 128 lipid system, meaning that the bilayer split off
into two separate pieces.

Is there a way to have the script avoid reducing the number of lipids in
the system in my original method?

I will deeply appreciate your assistance!

-Sanim Rahman
-- 
Gromacs Users mailing list

* Please search the archive at 
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