Hello,
I have been trying to perform a simulation of an alanine dipeptide chain in water using the Amoeba force field, but I have been having some difficulties with the minimization step. Specifically, I have been trying to use the following input file:
Minimization of Ala dipeptide for Amoeba
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 1000,
cut = 8,
iamoeba = 1,
jfastw = 4,
noshakemask=':1,2',
/
&amoeba
dipole_scf_tol=1e-6,
do_vdw_longrange = 1,
amoeba_verbose = 1,
/
&ewald
order = 5,
ew_coeff = 0.45,
nfft1 = 60,
nfft2 = 60,
nfft3 = 60,
/
Upon using this input I get the following output:
-------------------------------------------------------
Amber 16 SANDER 2016
-------------------------------------------------------
| Run on 12/07/2017 at 10:29:47
| Executable path: sander.MPI
| Working directory: /uufs/chpc.utah.edu/common/home/u0916868/Amoeba/Ala_Ala
| Hostname: kp329
[-O]verwriting output
File Assignments:
| MDIN: Min.in
| MDOUT: Min.mdout
|INPCRD: Ala-Ala.inpcrd
| PARM: Ala-Ala.prmtop
|RESTRT: Min.rst7
| REFC: Ala-Ala.inpcrd
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
| REMLOG: rem.log
| REMTYPE: rem.type
| REMSTRIP:
| SAVEENE: saveene
|CLUSTERINF: cluster.info
| RESERVOIR: reserv/frame
| REMDDIM:
Here is the input file:
Minimization of Ala dipeptide for Amoeba
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 1000,
cut = 8,
iamoeba = 1,
jfastw = 4,
noshakemask=':1,2',
/
&amoeba
dipole_scf_tol=1e-6,
do_vdw_longrange = 1,
amoeba_verbose = 1,
/
&ewald
order = 5,
ew_coeff = 0.45,
nfft1 = 60,
nfft2 = 60,
nfft3 = 60,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 15.270
And the following error:
The following have been reloaded with a version change:
1) amber/15 => amber/16 3) intel/2016.3.210 => intel/2017.4.196
2) impi/5.1.3 => impi/2017.4.196
forrtl: severe (24): end-of-file during read, unit 5, file /uufs/chpc.utah.edu/common/home/u0916868/Amoeba/Ala_Ala/Min.in
Image PC Routine Line Source
libifcoremt.so.5 00002B6B4BE6198F for__io_return Unknown Unknown
libifcoremt.so.5 00002B6B4BEAEFB9 for_read_seq_nml Unknown Unknown
sander.MPI 0000000000A22AF9 amoeba_mdin_mp_am Unknown Unknown
sander.MPI 000000000069D283 mdread1_ Unknown Unknown
sander.MPI 000000000063D2E4 sander_ Unknown Unknown
sander.MPI 000000000063CD4E MAIN__ Unknown Unknown
sander.MPI 0000000000466DDE main Unknown Unknown
libc-2.17.so 00002B6B4CC2EC05 __libc_start_main Unknown Unknown
sander.MPI 0000000000466CE9 Unknown Unknown Unknown
I created my inpcrd and prmtop files by following the example in section 17.2 in the Amber Manual, after making the system in xleap. Is there an error in my input file or the initial setup that I am missing, or are there lines that are missing from the input file?
Thanks for all the help,
Chase Zagorec-Marks
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Received on Thu Dec 07 2017 - 10:00:03 PST
