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Biomolecular simulation trajectory/data analysis.
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Local structure index of water (LSI) code issue #1043

Open Saqlain5565 opened 1 year ago

Saqlain5565 commented 1 year ago

i have been trying to get Local structure index (LSI) of water TIP4P/EW by running NPT through cpptraj by using following commands.

parm tip4p/ew.parm7 trajin eq_npt.nc solvent :WAT hbond watcoord out water_coordination.dat run

but following warning comes without output file.

Warning: Nothing selected for hydrogen bond analysis. Warning: Setup incomplete for [hbond]: Skipping

Warning: Set 'WATcoord[UU]' contains no data. Warning: File 'water_coordination.dat' has no sets containing data.

can anyone tell me where the problem is?

or can provide correct code to get LSI of water .

drroe commented 1 year ago

By default, cpptraj will only look for solute-solute hydrogen bonds. If you want to explicitly look at water-water hydrogen bonds, you need to explicitly specify the water donors and acceptors:

hbond watcoord donormask :WAT@O acceptormask :WAT@O image out nhbvtime.dat avgout hbavg.dat

You probably want the image keyword so you can capture hydrogen bonds that cross unit cell boundaries. Note that this will produce tons of information in the avgout file, since every existing water-water hydrogen bond will be reported. It will also be fairly slow, so you may want to use the OpenMP or MPI/OpenMP hybrid code to speed things up.

Let me know if this helps.

Saqlain5565 commented 1 year ago

Hello,

Thanks for the response.

what if i want to give specific boundary condition on 3.7Å ? then how can i change in that code ?

보낸 사람: Daniel R. Roe @.> 보낸 날짜: 2023년 8월 3일 목요일 오후 9:39 받는 사람: Amber-MD/cpptraj @.> 참조: Zafar,Muhammad Saqlain @.>; Author @.> 제목: Re: [Amber-MD/cpptraj] Local structure index of water (LSI) code issue (Issue #1043)

By default, cpptraj will only look for solute-solute hydrogen bonds. If you want to explicitly look at water-water hydrogen bonds, you need to explicitly specify the water donors and acceptors:

hbond watcoord donormask @. acceptormask @. image out nhbvtime.dat avgout hbavg.dat

You probably want the image keyword so you can capture hydrogen bonds that cross unit cell boundaries. Note that this will produce tons of information in the avgout file, since every existing water-water hydrogen bond will be reported. It will also be fairly slow, so you may want to use the OpenMP or MPI/OpenMP hybrid code to speed things up.

Let me know if this helps.

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Saqlain5565 commented 1 year ago

The code provide the out.dat files which contains the avg angle 165 apx. but the Angle Cutoff = 135.000.

so is it acceptable to have angle apx 165?