[gmx-users] PBC fix for visualization

[Mohsen Ramezanpour]

Hi Dallas and other Gromacs users,

I used -pbc whole and -ur compact in the first step
"System" index group

And then, used the output file for -pbc cluster.
Choosing the "System" index for clustering gave the best result I got.
(Although there are still few lipids which are not completely in the places
they should be).

Anyway, the outputs are reasonable. However, I have ca. 100 simulation
systems each of ca. 500 ns. (each system composed of ca. 4000 molecules)
Doing this clustering on the whole system takes a considerable time.

I thought I might be able to do the clustering on a group of atoms (an
index group composed of P in lipids and O in water molecules).
This, however, did not work and gmx trjconv complained about:

"Molecule 1 marked for clustering but not atom 1 in it - check your index!"

I was wondering what would be your solution to this?

Cheers,
Mohsen

On Mon, May 22, 2017 at 11:45 AM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Hi Dallas,
>
> Thanks for your reply.
> I did try -pbc cluster for waters. It could fix it somehow but not
> completely.
> After that, I had to use -pbc center to fix it. Still, I do not get what I
> want.
> Unfortunately, some waters and lipids are appearing from the other side of
> the box.
>
> Cheers,
> Mohsen
>
>
> On Sun, May 21, 2017 at 8:12 PM, Dallas Warren <dallas.warren at monash.edu>
> wrote:
>
>> I have found the cluster option of -pbc to work well for putting
>> aggregates back together correctly. Some times you do need an index
>> file and appropriate groups to assist with it getting it right.
>>
>> gmx trjconv -pbc cluster
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.warren at monash.edu
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to resemble
>> a nail.
>>
>>
>> On 16 May 2017 at 07:50, Mohsen Ramezanpour
>> <ramezanpour.mohsen at gmail.com> wrote:
>> > Dear Gromacs users,
>> >
>> > I have an HII phase made of one inverted cylinder (and waters inside)
>> in a
>> > triclinic box with 90, 90, 60 angles. After running the simulation, this
>> > cylinder become bent like a curve. I.e. is not a perfect cylinder
>> anymore.
>> > As a result, some water molecules and lipids pass the box sides and
>> enter
>> > from the other side of box because of PBC.
>> > Now, I want to make the cylinder again but I am not sure how to do so.
>> >
>> > The best I could do was to use "-pbc mol  -ur compact" options in
>> trjconv.
>> > However, here are still some lipids and molecules which are not part of
>> the
>> > cylinder.
>> >
>> > Any idea how could I fix the effect of these PBC in visualization?
>> >
>> > Thanks
>> > Mohsen
>> >
>> > --
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>
>
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-- 
*Rewards work better than punishment ...*