[gmx-users] Some Issues on Substrates/PBC

[Justin A. Lemkul]

André Farias de Moura wrote:
> Hi Michael,
> if you are not interested in the substrate dynamics, then you could try
> the freeze group options (freezegrps and freezedim). I have used these
> options for graphite and it worked just fine.
> best,
> André
> 

In addition to that, you may consider using pbc = full to get an infinite system 
and potentially avoid some of those edge effects it looks like you are seeing. 
I know others have used that kind of setup with carbon nanotubes (not my area of 
expertise, but I've read the discussions).

-Justin

> 
>> Dear Listmembers,
>>
>> This post is quite lengthy because it contains several different problems
>> that
>> I came across during my simulations and that I cannot figure out up to
>> now. I
>> included some links to pictures to give you some visualization and would
>> be
>> glad for every suggestion or hint even to part of my problems.
>>
>> Generally for my simulations I need substrates of silicon oxide and
>> graphite
>> (each one in different simulations). The substrate fills the simulation
>> box
>> completely in x-y direction so it should look like an infinite surface
>> considering the periodic boundary conditions.
>>
>> The simulation with silicon oxide is working fine but I experienced some
>> strange thing though: When the .gro file contains negative coordinates and
>> I
>> generate a .tpr for 4 nodes the structure is messed up totally after
>> energy
>> minimization (although it converges and gives no errors). I guess that the
>> breaking up in four parts is somehow connected to the 4 nodes, because
>> generating and running a 1 node .tpr solves this problem and the structure
>> keeps intact after em - see pictures here: ( http://tinyurl.com/59zfda ).
>> When
>> I shift the coordinates in the .gro with editconf so that every coordinate
>> is
>> positive the structure can be em with both 1 or 4 node without problems.
>>
>> For the main md I have to stick with 1 node anyway because I get a "Shake
>> block crossing node boundaries" error when I try to use 4 nodes. I found
>> the
>> advise to use less nodes in the mailing list archives and as I said it
>> works
>> for me, too, but is there any other way to get around this? For the test
>> runs
>> I'm doing now 1 node is fine, but for the real simulations later on I
>> would
>> like to use more nodes because the system will get bigger...
>>
>> With the graphite I have another problem: Again I have to stick with only
>> one
>> node, otherwise the structure is broken after energy minimization (with 4
>> nodes http://tinyurl.com/5eqngz ). Additionally here the energy
>> minimization
>> is not converging even after 2500 steps, forces keep in the range of 10^4
>> but
>> I can still do a md with this file that is not exploding (md with the
>> starting
>> structure without any energy minimization will result in an exploding
>> system
>> as one might expect). After energy minimization the graphite sheets (four
>> are
>> in the simulation) are bended up/down correspondently to the connected
>> periodic boundary at the edges of the simulation box (box is triclinic,
>> http://tinyurl.com/5m72ke ). When I run an md with this as starting
>> structure
>> without position restraints on the carbon atoms, the sheets cleave
>> beginning
>> from the edges and then reunite in a curled conformation within 10ps (
>> http://tinyurl.com/5j4l3z ).
>>
>> If I put position restraints on all carbon atoms the graphite keeps flat,
>> but
>> of course I still have the up/down bending at the box edges, which I also
>> want
>> to get rid off to have a real "infinite" graphite surface.
>>
>> First I thought that this was maybe a problem of my graphite structure not
>> fitting into my simulation box (hence the curling of the surface) but I
>> checked the bonding lengths and b0 in the topology, the unit cell vectors
>> and
>> box vectors thoroughly and everything seems to be right. If I copy my
>> simulation box and shift it by one of the box vectors I get a perfect
>> continuation without any deviation on the boundaries, so everything seems
>> like
>> it should be for the starting structure.
>>
>> I also simulated the same graphite sheets within a bigger box, so that
>> border
>> carbons could not feel their counterparts over the periodic boundaries.
>> That
>> gave no distortion at the edges after em and the em converged, but of
>> course
>> in this way I cannot get an continous surface.
>>
>> Even stranger is, that after em the whole structure coordinates are
>> shifted
>> into the neighbouring periodic cell! For a bigger system with some
>> additionally molecules that should absorb to the graphite surface the
>> graphite
>> sheets even ended up in different periodic images of the simulation box
>> after
>> em ( http://tinyurl.com/5uaxfa ). Maybe that's more a visualization
>> problem
>> because the following md simulation shows, that the molecules adsorb to
>> the
>> surface nevertheless (as one would suggest from pbc). Of course I can
>> reconfigure my .gro for visualization by substracting or adding the box
>> vectors untill all atoms end up inside the 'real' simulation box, but is
>> it
>> really supposed to behave that way, or is there something definitely wrong
>> with my structure?
>>
>> I saw this "shifting" of the whole substrate into another periodic image
>> of
>> the simulation box also in the simulation with the silicon substrate: it
>> 'jumped' into the periodic cell and then jumped back one frame later.
>> The other present (small) molecules stayed in the real simulation box all
>> the
>> time. I guess that this is maybe a problem caused by the substrate
>> "molecule"
>> filling up the whole simulation cell (at least in xy), but is there a way
>> of
>> getting Gromacs to always write out coordinates that lie within the real
>> simulation cell instead of an periodic image?
>>
>> And is there a way of defining bonds over the periodic boundaries? When I
>> tried this it always seemed as if Gromacs interpreted these bonds as
>> extremly
>> overstretched bonds (that are stretched over the whole simulation box
>> instead of just reaching the "short way" over the periodic boundary)
>> yielding
>> crippled structures ( http://tinyurl.com/54uvs4 ).
>>
>> All simulations used the ffG43b1 force field. Cutoffs of 1.2 and an Rlist
>> of
>> 1.4. Coulomb was shifted from 0.0 and VdW from 0.9. Timestep was 2 fs and
>> pbc
>> = xyz. The boxes were large in z direction to generate xy pbc. I can also
>> put
>> the topologies online if someone would like to look at them.
>>
>> I hope anyone can give me some advice because although I tried a lot of
>> things
>> right now I feel not like coming  close to a solution for my problems. :(
>>
>> Best regards,
>>     Michael
>> --
>> http://www.defux.de
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> 
> 
> &*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&
> Prof. Dr. André Farias de Moura
> Departamento de Química
> Universidade Federal de São Carlos
> São Carlos - SP - Brasil
> tel. 16-3351-8090
> &*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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