Dear Prof Case,
Thanks for always helping out with crucial suggestions along the way.
So, I did try to turn off the softcore potentials, and my simulation crashes. I later realized ( though I may be wrong) that the ifsc=1 supports dual topology, but setting ifsc=0 wont work as I need to create old style prmtp files with dummy atoms. I mean I need to redo from scratch I guess I am stuck!
Your second and third questions: Are you constraints between soft-core and non-soft-core atoms? Have you run the cpu version of pmemd, rather than GPU. Have you re-ordered the restraints in the
DISANG file to see if what is printed depends on that.
Yes, my distance restraints are between soft core and non-soft core atoms , as I am trying to apply distance restraints to keep my probe isopropanol in the kinase pocket and using 3 CA atoms as distance tether points.
I ran the cpu version of pmemd and surprisingly I see that Nstep 1 all energies are printed and evrtything looks okay but after 2 hours of wait no error is printed but my simulation does not proceed either, its stagnated at Nstep1.
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 84.482 Box Y = 81.908 Box Z = 87.672
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 96 NFFT2 = 96 NFFT3 = 96
Cutoff= 11.000 Tol =0.100E-04
Ewald Coefficient = 0.24861
Interpolation order = 4
| PMEMD ewald parallel performance parameters:
| block_fft = 0
| fft_blk_y_divisor = 2
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320
TI Mask 1 :IPA; matches 12 atoms
TI Mask 2 matches 0 atoms
TI region 1: 50200 atoms
TI region 2: 50188 atoms
SC Mask 1 :IPA; matches 12 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
DUMPFREQ 1 0 0.000000 0.000000 0 0
** No weight changes given **
RESTRAINTS:
Requested file redirections:
DISANG = output.disang
DUMPAVE = dist_0.00922.dat
LISTIN = POUT
LISTOUT = POUT
Restraints will be read from file: output.disang
Here are comments from the DISANG input file:
******
C2 ( 4396)-CA ( 204) NSTEP1= 0 NSTEP2= 0
R1 = 5.608 R2 = 6.108 R3 = 6.108 R4 = 6.608 RK2 = 30.000 RK3 = 30.000
Rcurr: 6.124 Rcurr-(R2+R3)/2: 0.016 MIN(Rcurr-R2,Rcurr-R3): 0.016
******
C2 ( 4396)-CA ( 2132) NSTEP1= 0 NSTEP2= 0
R1 = 6.333 R2 = 6.833 R3 = 6.833 R4 = 7.333 RK2 = 30.000 RK3 = 30.000
Rcurr: 6.864 Rcurr-(R2+R3)/2: 0.032 MIN(Rcurr-R2,Rcurr-R3): 0.032
******
C2 ( 4396)-CA ( 1387) NSTEP1= 0 NSTEP2= 0
R1 = 5.166 R2 = 5.666 R3 = 5.666 R4 = 6.166 RK2 = 30.000 RK3 = 30.000
Rcurr: 5.654 Rcurr-(R2+R3)/2: 0.011 MIN(Rcurr-R2,Rcurr-R3): 0.011
Number of restraints read = 3
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 15264
Number of shake restraints removed in TI region 1 : 0
Number of shake restraints removed in TI region 2 : 0
Sum of charges for TI region 1 = -0.00000008
Forcing neutrality...
Sum of charges for TI region 2 = -0.00000008
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 2920542
| Integers 2660910
| Nonbonded Pairs Initial Allocation: 2080476
| Running AMBER/MPI version on 12 MPI task
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8168E-11 at 2.732560
---------------------------------------------------
APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.30
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.78
|---------------------------------------------------
DOF for the SC part 1 of the system: 36
| TI region 1
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -204667.1974 EKtot = 0.0000 EPtot = -204667.1974
BOND = 16523.9408 ANGLE = 632.8186 DIHED = 3083.2720
1-4 NB = 878.2539 1-4 EEL = 11234.5634 VDWAALS = 44261.6846
EELEC = -281281.7307 EHBOND = 0.0000 RESTRAINT = 0.0000
DV/DL = 16.6912
Ewald error estimate: 0.1526E-03
------------------------------------------------------------------------------
Sent from Mail<
https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: David A Case<mailto:david.case.rutgers.edu>
Sent: 02 November 2020 07:20
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] NMR restraints
On Sun, Nov 01, 2020, Debarati DasGupta wrote:
>I am *not* understanding why is that when I used the TI masks and setting
>up icfe=1 with softcore potentials the NMR restraint energies all were
>zero in all steps of my minimization.
>Any suggestions as to how to troubleshoot this.
Did you try with TI but without softcore? Again, you just need to do a
single step to see what is happening. Are you constraints between
soft-core and non-soft-core atoms? Have you run the cpu version of
pmemd, rather than GPU. Have you re-ordered the restraints in the
DISANG file to see if what is printed depends on that. etc, etc.
I think you are experienced enough by now to do a lot of debugging on
your own. Remember that the goal is to find the minimal difference
between a run that seems to be doing what you want, and one that does
not.
....dac
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Received on Mon Nov 02 2020 - 14:30:02 PST
