[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

Anurag Dobhal anurag.dobhal at nano-medicine.co.in
Fri Oct 3 12:21:30 CEST 2014


hello Justin thanks for your reply.

I am unable to understand how to proceed in this tutorial. I am working on
it from many days but I am unable to do.

I have understood till the step.

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

this is the result which I got.

Area per protein: 2 nm^2
Area per lipid: 10.4716089904762 nm^2

Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 10.4755772444444 nm^2

Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 10.4716089904762 nm^2

Writing Area per lipid...
Done!


and the minimization step after that. I get the confout.gro file.


I am confused how to continue from the step

"perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat"

how many times do we need to run this command, nd with what changes ????

and how to solvate the system  ( which file ) and what will be the command ???

looking for your kind reply.

please help.

Thank you



On Thu, Oct 2, 2014 at 10:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/2/14 12:51 PM, Anurag Dobhal wrote:
>
>> how will I get to know that the system have shrunken enough, and which
>> file
>> I need to solvate.
>>
>>
> This is stated in the tutorial.
>
>
> -Justin
>
> --
> ==================================================
>
> 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.
>

-- 


*DISCLAIMER:*

*This communication is intended only for the person or entity to which it 
is addressed and may contain confidential and / or privileged material. Any 
review, retransmission, dissemination or other use is prohibited. If you 
have received this in error, please contact the sender and delete this 
material from your computer. Kindly note that this mail does not constitute 
an offer or solicitation for the purchase or sale of any financial 
instrument or as an official confirmation of any transaction. The 
information is not warranted as to completeness or accuracy and is subject 
to change without notice. Any comments or statements made herein do not 
necessarily reflect those of Nanomedicine Research Group.  Before opening 
the email or accessing any attachments, please check and scan for virus.*


More information about the gromacs.org_gmx-users mailing list