I think it's likely to be something in your parameters rather than input
files. You don't say how you obtained them though.
On Wed, Aug 1, 2018, 1:46 PM David Stevens <david.stevens.drs73.yale.edu>
wrote:
> Dear AMBER community,
>
> For the past two months I have been trying to perform a simple MD
> simulation on dTMP. Attached is a picture of the structure and the .inpcrd
> and .prmtop files that I used. The issue that I am encountering is that my
> structure is imploding upon the NPT heating and NPT equilibration
> sections. It almost seems like I am encountering a parameter issue (the
> bonds and angles are going crazy). The structure is totally fine prior to
> the heating phase (after minimizing the solvent, hydrogens, etc)
>
> The system is literally: 1 dTMP, 0.15 M Na/Cl, and a water box.
>
> Prior to NPT heating the structure looks like this. Which looks fine.
>
>
> The following is after NPT heating (all residues within 3 angstroms of
> resid 1 (dTMP) is shown)
>
> This is another angle to see the distortion better (same frame)
>
>
> The following is after NPT equilibration.
>
>
> The following is my npt_heat.in file:
>
> First NPT running
>
> &cntrl
>
> imin=0, irest=0,
>
> nstlim=360000, dt=0.001, ntx=1,
>
> ntpr=500, ntwx=5000, ntwr=5000,
>
> cut=10, ntb=2, ntp=1, pres0=1.01325,
>
> ntc=2, ntf=2,
>
> ntt=3, gamma_ln=2.0, ig=-1,
>
> tempi=0.0, temp0=300.0,
>
> ioutfm=1, ntwv=-1, ig=-1, iwrap=1,
>
> nmropt=1,
>
> /
>
> &wt type='TEMP0', istep1=0, istep2=10000, value1=0.0, value2=50.0 /
>
> &wt type='TEMP0', istep1=10001, istep2=60000, value1=50.0, value2=50.0 /
>
> &wt type='TEMP0', istep1=60001, istep2=70000, value1=50.0, value2=100.0 /
>
> &wt type='TEMP0', istep1=70001, istep2=120000, value1=100.0, value2=100.0 /
>
> &wt type='TEMP0', istep1=120001, istep2=130000, value1=100.0, value2=150.0
> /
>
> &wt type='TEMP0', istep1=130001, istep2=180000, value1=150.0, value2=150.0
> /
>
> &wt type='TEMP0', istep1=180001, istep2=190000, value1=150.0, value2=200.0
> /
>
> &wt type='TEMP0', istep1=190001, istep2=240000, value1=200.0, value2=200.0
> /
>
> &wt type='TEMP0', istep1=240001, istep2=250000, value1=200.0, value2=250.0
> /
>
> &wt type='TEMP0', istep1=250001, istep2=300000, value1=250.0, value2=250.0
> /
>
> &wt type='TEMP0', istep1=300001, istep2=310000, value1=250.0, value2=300.0
> /
>
> &wt type='TEMP0', istep1=310001, istep2=360000, value1=300.0, value2=300.0
> /
>
> &wt type='END' /
>
> The following is my npt_eq.in file:
>
> NPT equilibrium 2ns
>
> &cntrl
>
> imin=0, irest=1,
>
> nstlim=2000000, dt=0.001, ntx=7,
>
> ntpr=1000, ntwx=1000, ntwr=1000,
>
> cut=10, ntb=2, ntp=1, pres0=1.01325,
>
> ntc=2, ntf=2,
>
> ntt=3, gamma_ln=1.0,
>
> tempi=300.0, temp0=300.0,
>
> ioutfm=1, ntwv=-1, ig=-1, iwrap=1,
>
> I have tried recreating my .inpcrd and .prmtop files and still encounter
> the same issue. I usually run using AMBER CUDA, so I tried running this
> with CPUs, but that didn't work either. I am using Amber14/Ambertools
> 15.
>
> Thank you for your help,
>
> David
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Received on Thu Aug 02 2018 - 05:30:03 PDT
