Hi Zhen,
Thanks for your valuable suggestion. I changed the smd.in and disang.in
as you mentioned.
smd.in
&cntrl
imin=0, irest=1, ntx=5,
nstlim=500000, dt=0.002,
ntc=2, ntf=2, temp0=300.0,
ntpr=500, ntwx=500, ntwr=5000,
cut=10.0,
nmropt=1,
/
# --- Control time-dependent behavior
&wt type='DUMPFREQ', istep1=500 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=1 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=2 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=3 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=4 /
&wt type='END' /
&end
DISANG=disang.in
DUMPAVE=mdpull.dat
disang.in
# disang.in -- Time-dependent restraints for SMD pulling of 3 H-bonds
# --- Define the restrained atom pairs (Donor-Acceptor)
&rst iat=14468,13467, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
ir6=1, ifvar=1 /
&rst iat=14448,13473, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
ir6=1, ifvar=2 /
&rst iat=14423,13512, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
ir6=1, ifvar=3 /
&rst iat=14429,13492, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
ir6=1, ifvar=4 /
Now the output files stop before starting the SMD. The output is given
below:
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 45.831
| New format PARM file being parsed.
| Version = 1.000 Date = 08/08/25 Time = 18:49:53
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting box info from netcdf restart file
NATOM = 109569 NTYPES = 22 NBONH = 101939 MBONA = 7649
NTHETH = 16141 MTHETA = 10514 NPHIH = 32966 MPHIA = 31743
NHPARM = 0 NPARM = 0 NNB = 206998 NRES = 32709
NBONA = 7649 NTHETA = 10514 NPHIA = 31743 NUMBND = 114
NUMANG = 261 NPTRA = 245 NATYP = 51 NPHB = 1
IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Can you please check the output and give suggestions?
Thanks,
Abhisek Jana
Department of Chemistry
IIT Bombay
On 2025-10-27 18:53, Li, Zhen via AMBER wrote:
> Hi Abhishek,
>
> To my understanding, you need to do the two changes:
>
> 1.
> Rewrite the &wt block as
> # --- Control time-dependent behavior
> &wt type='DUMPFREQ', istep1=500 /
> &wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
> ivar=1 /
> &wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
> ivar=2 /
> &wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
> ivar=3 /
> &wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
> ivar=4 /
> &wt type='END' /
> &end
> 2.
> Move the &wt block from disang.in to smd.in (between lines "/" and
> "DISANG=disang.in"), so disang.in only has the &rst block.
>
> Please let me know whether this modification solved the issue.
>
> Best regards,
> Zhen.
>
> 1.
>
> _____________________
>
> Zhen Li<http://lizhen62017.wixsite.com/home>, Ph.D.,
>
> The Merz Research Group<http://merzgroup.org>,
>
> Michigan State University,
>
> Cleveland Clinic.
>
> ________________________________
> From: Abhisek Jana via AMBER <amber.ambermd.org>
> Sent: Monday, October 27, 2025 1:33 AM
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: [AMBER] Assistance with SMD Error Related to Hydrogen Bond
> Collective Variables
>
> Dear all,
>
> I am performing a steered molecular dynamics (SMD) simulation using
> hydrogen bond collective variables defined in the disang.in file.
> However, I am encountering the following error:
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
> default_name
> begin time read from input coords = 103200.000 ps
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> ERROR: No "wt" namelist with TYPE=END found
>
> I have attached the smd.in
> and disang.in files for your reference. I would greatly appreciate your
> feedback and suggestions on the possible cause of this error and how to
> resolve it.
>
> smd.in
>
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=500000, dt=0.002,
> ntc=2, ntf=2, temp0=300.0,
> ntpr=500, ntwx=500, ntwr=5000,
> cut=10.0,
> nmropt=1,
> /
> DISANG=disang.in
> DUMPAVE=mdpull.dat
>
> disang.in
>
> # disang.in--Time-dependent restraints for SMD pulling of 3 H-bonds
>
> # --- Define the restrained atom pairs (Donor-Acceptor)
> &rst iat=14468,13467, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
> ir6=1, ifvar=1 /
> &rst iat=14448,13473, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
> ir6=1, ifvar=2 /
> &rst iat=14423,13512, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
> ir6=1, ifvar=3 /
> &rst iat=14429,13492, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
> ir6=1, ifvar=4 /
>
> # --- Control time-dependent behavior
> &wt type='DUMPFREQ', istep1=500 /
> &wt type='END' /
> &wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
> ivar=1 /
> &wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
> ivar=2 /
> &wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
> ivar=3 /
> &wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
> ivar=4 /
> &end
>
> Best regards,
>
> Abhisek Jana
>
> Institute Postdoctoral Fellow
>
> Department of Chemistry, IIT Bombay
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Received on Mon Oct 27 2025 - 22:00:02 PDT
