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 Tue May 23 2023 - 13:30:02 PDT
