Hi,
I don't know why it said 100 steepest-decent steps but based on the input file, 2500 steepest-descent steps are performed before switching to the conjugate gradient method ( another 2500 steps).So, you have 5000 steps totally.
For stability purposes, we can start with a smaller dt and then increase it in the next step of equilibrium.
Best,
Masoud
________________________________
From: HAFIDAH ZAKI AL QUDAH via AMBER <amber.ambermd.org>
Sent: Monday, August 5, 2024 15:09
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] CHARMM-GUI-provided scripts
Hello,
I would like to know the NCYC value that determines the number of steps for the steepest descent from the CHARMM-GUI-provided minimization scripts for AMBER MD simulation. Is it 2500 or 100 steps because the provided script is:
! Minimization options
imin=1, ! Turn on minimization
maxcyc=5000, ! Maximum number of minimization cycles
ncyc=2500, ! 100 steepest-descent steps, better for strained systems
Additionally, I would like to inquire about the applied restraint value in the CHARMM-GUI-provided minimization and equilibration scripts for AMBER MD simulation. Furthermore, I am interested in knowing the specific atoms for which the strain was applied. The obtained script:
! Restraint options
ntr=1, ! Positional restraints for proteins, sugars, and ligands
! Set water atom/residue names for SETTLE recognition
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
/
&ewald
vdwmeth = 0,
/
Protein posres
1.0
RES 1 296 297 297
END
END
Finally, I would like to understand how the SHAKE constraint was applied even though the time step was 1 fs (dt=0.001) in the equilibration script provided by CHARMM-GUI for the AMBER MD simulation as follows:
! MD settings
nstlim=125000, ! 125K steps, 125 ps total
dt=0.001, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=2, ! Do not calculate forces of bonds containing hydrogen
Looking forward to hearing from you. Thanks!
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7Ckeramati.m%40northeastern.edu%7C4f99fe54dd154f72702008dcb5824cbb%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638584818447184347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=qOPHCoZ767dAOP6Os%2FGKZf3K973NcuxV1vj8KMaTBzU%3D&reserved=0<
http://lists.ambermd.org/mailman/listinfo/amber>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 05 2024 - 12:30:02 PDT
