Re: [AMBER] AMBER error vlimit exceed for step

From: He, Amy via AMBER <amber.ambermd.org>
Date: Sat, 9 Mar 2024 02:26:42 +0000

Hey Vero,

There could be different reasons for getting vlim exceed in dynamics simulations for TI. I have some experience with this, but other more experienced users might be able to give you better advice.
Here’re two things I would suggest:

Inspect the minimized structure
Is the minimized structure visibly distorted outside of the soft-core region? If so you might want to reassign the soft-core (see below). Also, even though the minimization could be run on a different lambda, it’s best to keep it the same as the designated value in the production runs.

Consider the assignment of soft-core region
I noticed THAT you had only 2 softcore atoms. If you’re running dual-top TI, then one of them is disappearing and the other is appearing. In that case, You might want to try including some more atoms in the soft-core region, like the directly bonded atoms.
Previously, I observed distorted imidazole rings in histidine residues, when I included only the dissociable H atom in the soft-core region. I was able to solve this after including the nitrogen atoms and adjusting the SHAKE-enabled region. But this might depend on the exact scaling scheme you are following for the soft-core region and how it is embedded in the surrounding system.

If you could provide a little more information on your system and your protocol, other members on this list server will be able to provide more specific suggestions :>


Hope this helps! 


--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: VERONICA MARTIN HERNANDEZ via AMBER <amber.ambermd.org>
Date: Friday, March 8, 2024 at 11:20 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] AMBER error vlimit exceed for step
Hi everyone
I was performing TI calculations and the minimization went well, with the following output:
                    FINAL RESULTS
| TI region  1
   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
 ******      -1.3744E+05     7.8915E-03     5.6513E-01     H2      24706
 BOND    =    11603.4879  ANGLE   =       22.1290  DIHED      =       21.1698
 VDWAALS =    33301.1213  EEL     =  -182346.6482  HBOND      =        0.0000
 1-4 VDW =        6.6181  1-4 EEL =      -46.4153  RESTRAINT  =        0.0000
 DV/DL  =       -22.0427
  Softcore part of the system:       2 atoms,       TEMP(K)    =           0.00
 SC_Etot=         0.0000  SC_EKtot=         0.0000  SC_EPtot   =         1.7742
 SC_BOND=         0.0025  SC_ANGLE=         0.0554  SC_DIHED   =         0.0021
 SC_14NB=         0.0000  SC_14EEL=         0.0000  SC_VDW     =        -0.0011
 SC_EEL =         1.7154
 SC_RES_DIST=     0.0000  SC_RES_ANG=       0.0000  SC_RES_TORS=         0.0000
 SC_EEL_DER=      0.4021  SC_VDW_DER=       0.1780  SC_DERIV   =         0.5801
 ------------------------------------------------------------------------------
| TI region  2
   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
 ******      -1.3744E+05     7.8915E-03     5.6513E-01     H2      24706
 BOND    =    11603.4879  ANGLE   =       22.1290  DIHED      =       21.1698
 VDWAALS =    33301.1213  EEL     =  -182346.6482  HBOND      =        0.0000
 1-4 VDW =        6.6181  1-4 EEL =      -46.4153  RESTRAINT  =        0.0000
 DV/DL  =       -22.0427
  Softcore part of the system:       2 atoms,       TEMP(K)    =           0.00
 SC_Etot=         0.0000  SC_EKtot=         0.0000  SC_EPtot   =         0.9330
 SC_BOND=         0.0003  SC_ANGLE=         0.2909  SC_DIHED   =         0.0021
 SC_14NB=         0.0000  SC_14EEL=         0.0000  SC_VDW     =        -0.0075
 SC_EEL =         0.6472
 SC_RES_DIST=     0.0000  SC_RES_ANG=       0.0000  SC_RES_TORS=         0.0000
 SC_EEL_DER=      0.4021  SC_VDW_DER=       0.1780  SC_DERIV   =         0.5801
But when I perform the equilibration step (I do it with pmemd and cpus) I have always got the error of vlimit exceed for step, even from step 0.
How can I solve it?
Thanks in advance
Vero
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Received on Fri Mar 08 2024 - 18:30:02 PST
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