Cnt Simulations

7/22/2019 Cnt Simulations

1/13

Goal: Conformational sampling ofpeptides under nanotube confinement.

Replica Exchange MD preferably in theNPT ensemble such that realistic ensemblesat higher temperature replicas are obtained


2/13

SD integrator(Langevin Thermostat),Berendsen Barostat

with the CNT modeled withbonded interactions

efine = -DPOSRES_CNT...ref_t = %8.3fPcoupl = Beren sen

All pressure coupling used areisotropic unless otherwise stated.


3/13

As can be

observed, something is notcor

Bonded CNT + sd + position restraints


4/13

Performed simulations with thebonded interactions of the nanotube.

Performed one set of simulations with po

This shows that the problem is

probably solely NOT with having position

restraints.

JM suggested that one can use minimal position restraints such as restr


5/13

Position restraints (with bonded information

Con: The temperature of the

CNT group severelyunderestimated. The temperature of thesystem is affected.


6/13

Bonded CNT + md + nose-hoover + positio

Pros:The mean output temperatures match the set

temperatures.The mean diameter seems to be close to what it should

be.

The pressure tensors seem not so absurd.

Cons:MD + nose-hoover + Berendsen: Not quite reliable as

per literature / GROMACS forum. grompp issues a warningUsing Berendsen pressure coupling invalidates the true

ensemble for the thermostat

CNT Protein

SOL


7/13

Bonded CNT + md + v-re

Pros:The mean diameter seems to be close to what it should

be.The pressure tensors seem not so absurd.

Cons:The temperature of the CNT does not match the output

temperature.Unsure about the validity of the ensemble using

md+v-rescale + berendsen barostat.

CNT Protein

SOLSystem


8/13

Bonded CNT

Pros:The temperature of the system stays close to the set

temperature especially at high temperatures

The pressure tensors seem not so absurd.

Cons:Unsure about the ensemble generated by md+v-rescale

+ berendsen barostat


9/13

Control simulation to note thatthe three different schemes ofpling yield different distributions of

ntial energies with the sd integratorhaving a shifted distribution

pared to the other two. The systemused was a box of water 5846

molecules


10/13

In this setup, the CNT wascoupled with a tau-t = 0.005 and theprotein and CNT were coupled with

tau-t = 1.0.

Pros.The temperature of the CNT

group seems to match the outputtemperature quite well.

Cons.The output Pressure tensors

seem to be unrealistic.tau-t=0.005 does not make

any sense.


11/13

Frozen CNT + position restraint

Pro: The mean outputtemperatures match the set temperatures.

The diamter remains constant

Con: The pressure tensorsseem absurd.


12/13

Pros.The temperatures of the

protein and the solvent aremaintained

Cons.No pressure coupling


13/13

In all the cases shown above, using parrinello-rahman barostat, the system crasheswith refcoord-scaling = COM. If refcoord-scaling is set to all we can use PR barostat whichis of course not a viable option since all the coordinates are scaled w.r.t to the box sizeand this would imply the diameters of the CNTs changed.Freezing the CNT, with the bonded information included is NOT a viable option (thesimulation crashes at step 0 with segmentation fault. However, if bonded information are notincluded, the simulations can be run with absurd pressure tensors.

A control simulation with only the CNT with the bonded interactions in CNT notconstrained, yielded nearly (eg., 304 K with 300 K as the set temperature) correct outputtemperature for the CNT group. However, when water and protein are included to such a systecrashed with LINCS error. Since such a modification (not constraining bonds yielding correcttemperatures) is absurd I did not pursue this avenue any further.

Documents

Cnt Simulations