## VMD-L Mailing List

**From:** Francesco Pietra (*chiendarret_at_gmail.com*)

**Date:** Sun Aug 23 2015 - 04:09:15 CDT

**Next message:**Atila Petrosian: "embedding proteins in membrane: child killed: segmentation violation"**Previous message:**Ozan Dernek: "Bader Charge Analysis"**In reply to:**Mayne, Christopher G: "Re: ffTK and geometry optimization level"**Next in thread:**Mayne, Christopher G: "Re: ffTK and geometry optimization level"**Reply:**Mayne, Christopher G: "Re: ffTK and geometry optimization level"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Chris:

Recalling that initially I carried out a successful geometry optimization

%chk=....chk

%nproc=16

%mem=120GB

# RHF/6-31G* Stable=Opt SCF=Tight Geom=PrintInputOrient

where the Stable=Opt avoided crashing because of unstable wavefunction,

before trying SFC/single-point MP2, I have now tried MP2 geometry

optimization by also writing on disk

%chk=....chk

%nproc=16

%mem=120GB

# MP2/6-31G* maxdisk=900GB MP2=SemiDirect guess=read geom=checkpoint

The procedure went on a lot, to nearly discarding MO integrals, crashing

without error messages as shown below:

JobTyp=2 Pass 1: I= 1 to 85.

(rs|ai) integrals will be sorted in core.

SymMOI: orbitals are not symmetric.

Spin components of T(2) and E(2):

alpha-alpha T2 = 0.1952657779D+00 E2= -0.6186401423D+00

alpha-beta T2 = 0.9897063485D+00 E2= -0.3241890891D+01

beta-beta T2 = 0.1941391244D+00 E2= -0.6171858226D+00

ANorm= 0.1542436790D+01

E2 = -0.4477716856D+01 EUMP2 = -0.18915535514164D+04

(S**2,0)= 0.49577D+00 (S**2,1)= 0.39665D+00

E(PUHF)= -0.18871168171D+04 E(PMP2)=

-0.18915915926D+04

Would need an additional 807073191 words for in-memory AO integral

storage.

DD1Dir will call FoFJK 6 times, MxPair= 3600

NAB= 7225 NAA= 3570 NBB= 3570 NumPrc= 16.

FoFJK: IHMeth= 1 ICntrl= 200 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F

IRaf= 990000000 NMat=3600 IRICut= 1297 DoRegI=F DoRafI=T ISym2E= 2.

E(PMP3)= -0.18916618537D+04

MP4(D)= -0.93363445D-01

MP4(S)= -0.58146163D-01

MP4(R+Q)= 0.84912525D-01

I do not understand whether " Would need an additional 807073191 words for

in-memory AO integral storage." is a normal messages or it implies that the

scratch disk could not be used to this purpose for these few words (ca

6GB). Or crashing occurred for a different reason. I did not repear

:Stable=Opt" for the MP2 procedure.

Although not a good excuse, I know Gaussian little, having always used

gamess-us (in this case I could have used many nodes with OpenMPI compiled

gamess-us)

thanks a lot

francesco

On Thu, Aug 20, 2015 at 8:09 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>

wrote:

*> Francesco,
*

*>
*

*> There are two places in the workflow where substituting MP2 geometry
*

*> optimization with SCP opt + MP2 single point would matter: determining a
*

*> low energy conformation of the molecule, and as input for the Hessian
*

*> calculation, which I'll deal with in order. Technically speaking, the ffTK
*

*> parser should handle the change in theory without a problem. You can check
*

*> this by loading the optimization log and checking that VMD reads in
*

*> multiple conformations into the OpenGL window. From a theoretical
*

*> perspective, as long as the resulting geometry is of sufficient energy it
*

*> should suffice for use in subsequent steps in the workflow, e.g., water
*

*> interaction profiles. Whether this works with the Hessian calculation is
*

*> less clear to me a priori, and may work for some cases but not others. The
*

*> input file for the Hessian calculations tells Gaussian to read the initial
*

*> coordinates from the checkpoint file output during the geometry
*

*> optimization. I could imagine that an SCP-computed geometry minimum may
*

*> differ from MP2 such that you would end up with problems in the
*

*> frequencies. I would have to run test cases to say much more.
*

*> Alternatively, if you think you have sufficient justification, you could
*

*> perform all calculations as the SCP level of theory, and the ffTK parsers
*

*> should continue to work (fingers crossed!).
*

*>
*

*> Regards,
*

*> Christopher Mayne
*

*>
*

*> On Aug 20, 2015, at 12:50 PM, Francesco Pietra wrote:
*

*>
*

*> Hi Chris:
*

*> Sorry for having missed your answer. I also came across those suggestions
*

*> by Gaussian, but that was not the reason. As I said it was lack of
*

*> sufficient memory.
*

*>
*

*> I still have to become comfortable with "divide and conquer". As it is
*

*> implied in your answer that it is of such accuracy as to demand OPT/MP2,
*

*> I'll try to learn how to do.
*

*>
*

*> At any event, would ffTK accept the Gaussian log file from geometry
*

*> optimization at SCF level, followed by single-point MP2? Or is ffTK
*

*> expecting a log for geometry optimization at MP2 level?
*

*>
*

*> Thanks a lot
*

*>
*

*> francesco
*

*>
*

*>
*

*>
*

*> On Thu, Aug 20, 2015 at 7:23 PM, Mayne, Christopher G <
*

*> cmayne2_at_illinois.edu> wrote:
*

*>
*

*>> Francesco,
*

*>>
*

*>> I responded here:
*

*>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/26205.html
*

*>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_mailing-5Flist_vmd-2Dl_26205.html&d=AwMFAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=-HlUTO-p5cBc5PIIWOaJ9-qnT28s75DUp7XlPlRi7DY&m=hckOdtohvEupU4CfzeFwAxpXzxhSco3vdYrhq7bfK9I&s=9Hol9P12g2oVy9_qFjZrZcrKadtHwLIAIthlZ1QQJtI&e=>
*

*>>
*

*>> MP2 is the level of theory prescribed by the CHARM General Force Field to
*

*>> accurately describe the internal dynamics of molecule. Further, it is
*

*>> generally accepted practice to take a "divide and conquer" approach to
*

*>> parameterize large ligands.
*

*>>
*

*>> Regards,
*

*>> Christopher Mayne
*

*>>
*

*>> On Aug 20, 2015, at 10:13 AM, Francesco Pietra wrote:
*

*>>
*

*>> Hello:
*

*>>
*

*>> I posted recently about ffTK OPT MP2 problems, no answer, however it
*

*>> became clear that the shared memory on a node (120GB) was not enough, and
*

*>> could not be increased. On the other hand, Gaussian is threaded, so that I
*

*>> can't exploit the enormous resources of the cluster.
*

*>>
*

*>> Therefore, my question is, is OPT at MP2 really needed for getting a good
*

*>> ff for ligands along ffTK in the realm of classical MD? OPT at SCF level,
*

*>> followed by single-point MP2 is not enough? I understand that it depends on
*

*>> what one is looking for, from simple docking to normal mode calculations,
*

*>> so that my question covers all situations.
*

*>>
*

*>> If SCF followed by single-point MP2 is not enough, the only alternative
*

*>> that I can see is to break the ligand into pieces and carry out OPT/MP2 on
*

*>> each piece, allowing for the approximations in reforming the whole ligand.
*

*>>
*

*>> Thanks a lot for advice on strategy.
*

*>>
*

*>> francesco pietra
*

*>>
*

*>>
*

*>>
*

*>
*

*>
*

**Next message:**Atila Petrosian: "embedding proteins in membrane: child killed: segmentation violation"**Previous message:**Ozan Dernek: "Bader Charge Analysis"**In reply to:**Mayne, Christopher G: "Re: ffTK and geometry optimization level"**Next in thread:**Mayne, Christopher G: "Re: ffTK and geometry optimization level"**Reply:**Mayne, Christopher G: "Re: ffTK and geometry optimization level"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]