I am just updating you on this issue to see if the snapshots' images can
help figure out the cause of the problem. Here is a link to three snapshots
taken at in difference of 50 steps (dt = 1fs):
https://www.dropbox.com/s/gkosa5zqyb2oyzp/warp_err.png?dl=0
The problem seems to occur when one of the free ligands is close to the
boundary, and wrapping it back in the box completely messes up the system.
Any suggestions on how to prevent it?
Best,
Mish
On Tue, May 23, 2023 at 2:59 PM mish <smncbr.gmail.com> wrote:
> Dear all,
>
> I had been struggling to make the LiGaMD simulation work in Amber, but
> something strange is happening with TI code of pmemd.duda (both in Amber20
> and 22).
>
>
> I have a system with 10 (:1-20) monosaccharides followed by a protein.
> res:1-2 is bound to protein and the rest of the 9 have been placed
> randomly in a solvent. I have worked a lot with this system and don't
> expect any issues in monosaccharide-bound proteins. In brief, Ihave nicely
> equilibrated system and as soon as I start LiGaMD (igamd = 10 or 11), the
> temperature increases rapidly within 50 steps of 1 fs dt, and simulation
> will eventually halt with "Periodic box dimensions have changed too much
> from their initial value". Error.
>
> | TI region 1
>
>
> NSTEP = 30 TIME(PS) = 5125.030 TEMP(K) = 387.34 PRESS =
> 0.0
> Etot = -22661.9869 EKtot = 29754.9336 EPtot =
> -52416.9205
> BOND = 41243.8967 ANGLE = 830.4927 DIHED =
> 1140.4110
> 1-4 NB = 350.8381 1-4 EEL = 5719.4739 VDWAALS =
> 16041.6620
> EELEC = -117743.6950 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
> 249195.5199
> Density =
> 1.0447
> DV/DL = 223.4563
>
> ------------------------------------------------------------------------------
>
> Softcore part of the system: 26 atoms, TEMP(K) =
> 57033.85
> SC_Etot= 62508.3446 SC_EKtot= 4420.1506 SC_EPtot =
> 58088.1940
> SC_BOND= 57361.0095 SC_ANGLE= 270.5395 SC_DIHED =
> 11.5852
> SC_14NB= 253.0552 SC_14EEL= 212.6062 SC_VDW =
> 2.7724
> SC_EEL = -23.3739
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS=
> 0.0000
> SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV =
> 0.2621
>
> ------------------------------------------------------------------------------
>
> TI_Etot= 0.0000 TI_EKtot= 0.0000 TI_EPtot =
> -39.6621
> TI_BOND= 0.0000 TI_ANGLE= 0.0000 TI_DIHED =
> 0.0000
> TI_14NB= 0.0000 TI_14EEL= 0.0000 TI_VDW =
> -17.0622
> TI_EEL = -22.5999
>
> ------------------------------------------------------------------------------
>
>
> | TI region 2
>
>
> NSTEP = 30 TIME(PS) = 5125.030 TEMP(K) = 330.14 PRESS =
> 0.0
> Etot = -27082.1375 EKtot = 25334.7830 EPtot =
> -52416.9205
> BOND = 41243.8967 ANGLE = 830.4927 DIHED =
> 1140.4110
> 1-4 NB = 350.8381 1-4 EEL = 5719.4739 VDWAALS =
> 16041.6620
> EELEC = -117743.6950 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
> 249195.5199
> Density =
> 1.0435
> DV/DL = 223.4563
>
> ------------------------------------------------------------------------------
>
>
> | TI region 1
>
>
> NSTEP = 40 TIME(PS) = 5125.040 TEMP(K) = 620.00 PRESS =
> 0.0
> Etot = ************** EKtot = 47626.9570 EPtot =
> **************
> BOND = 55934.2904 ANGLE = 1096.8148 DIHED =
> 1153.7867
> 1-4 NB = 386.6471 1-4 EEL = 5670.9891 VDWAALS =
> **************
> EELEC = -117711.6519 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
> 249195.5199
> Density =
> 1.0447
> DV/DL = **************
>
> ------------------------------------------------------------------------------
>
> Softcore part of the system: 26 atoms, TEMP(K) =
> 162292.45
> SC_Etot= 124368.6295 SC_EKtot= 12577.7417 SC_EPtot =
> 111790.8878
> SC_BOND= 108757.5814 SC_ANGLE= 723.5005 SC_DIHED =
> 13.2930
> SC_14NB= 2021.3141 SC_14EEL= 190.8677 SC_VDW =
> 70.7727
> SC_EEL = 13.5584
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS=
> 0.0000
> SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV =
> ***********
>
> ------------------------------------------------------------------------------
>
> TI_Etot= 0.0000 TI_EKtot= 0.0000 TI_EPtot =
> ***********
> TI_BOND= 0.0000 TI_ANGLE= 0.0000 TI_DIHED =
> 0.0000
> TI_14NB= 0.0000 TI_14EEL= 0.0000 TI_VDW =
> ***********
> TI_EEL = -12.3127
>
> ------------------------------------------------------------------------------
>
> My gamd input file is like the below:
>
> &cntrl
> imin=0, irest=1, ntx=5,
> ntt=3, gamma_ln=1.0, temp0=303.15,
> cut=9.0, nstlim=500000, dt=0.001,
> ntc=1, ntf=1,
> iwrap=1, barostat=2,
> ntp=1, pres0=1.0,
> ntpr=10, ntwx=50, ntwr=50000,
> ntxo=2, ioutfm=1,
>
> igamd = 11, irest_gamd = 0,
> ntcmd = 700000, nteb = 27300000, ntave = 140000,
> ntcmdprep = 280000, ntebprep = 280000,
> sigma0P = 4.0, sigma0D = 6.0, iEP = 2, iED=1,
> icfe = 1, ifsc = 1, gti_cpu_output = 0, gti_add_sc = 1,
> timask1 = ':1-2', scmask1 = ':1-2',
> timask2 = '', scmask2 = '',
> ibblig = 1, nlig = 10, atom_p = 667, atom_l = 19, dblig = 3.7,
> &end
>
>
> I figured out that this problem occurs even if I set igamd = 0 but will
> not occur if I set timask1 = ':2-3', scmask1 = ':2-3'. This occurs only
> when ligand residues 1–2 (a monosaacharide) bound to proteins is specified
> in the TI mask. Any ideas on how I can I figure out what is going wrong
> here? I am using Amber14SB and Glycam06 with TIP3P water box. Deleting all
> the keywords starting from igamd in MD input files (making it classical
> MD) also works fine, even on a microsecond scale.
>
>
> Best,
> Mish
>
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Received on Wed May 24 2023 - 11:00:03 PDT
