AMBER Archive (2006)

Subject: Re: AMBER: proper restart procedure?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed May 03 2006 - 06:48:25 CDT

I think it may be from using ntx=7. with ntb=0
you should use ntx=5.

it is also possible that the restart is corrupted or truncated.
use a text editor to look at it. The format is given on the
amber web page (look for amber file formats).

my other comments-
I have not had good luck with cut=12 and GB simulations.
I also recommend against igb=1 (especially for anything but a
short peptide) unless you have good reason to use this.
igb=5 is better (and be careful of which intrinsic radii
you choose, the "best" set depends on the igb value.
See work by Onufriev et al on these GB models.
carlos

John J. Love wrote:

> Hello Amber Users,
>
> I have tried to find a solution to the current problem I'm having in a
> number of places but I have not been successful. I believe this is a
> simple problem. I am having no success in restarting MD runs after an
> unplanned stop (crash). I have looked in the manuals, tutorials,
> archives, threads, etc. and have not found a solution. If you know of
> a reference source to solve this please let me know.
>
> The original sander command -
>
> $AMBERHOME/exe/sander -O -i W43Y_GB_md1.in -o W43Y_GB_md1.out -c
> W43Y_GB_init_min.rst -p W43Y.prmtop -r W43Y_GB_md1.rst -x
> W43Y_GB_md1.mdcrd
>
> This is the original input file -
>
> (Before)
>
> 10-mer DNA MD
>
> &cntrl
>
> imin = 0, ntb = 0,
>
> igb = 1, ntpr = 100, ntwx = 100,
>
> ntt = 1, gamma_ln = 1.0,
>
> tempi = 300.0, temp0 = 300.0,
>
> nstlim = 1500000, dt = 0.001,
>
> cut = 12
>
> /
>
> After the crash I have modified the input file as such
> (W43Y_GB_md1_rst.in) -
>
> (After)
>
> 10-mer DNA MD
>
> &cntrl
>
> imin = 0, irest=1, ntx=7, ntb = 0,
>
> igb = 1, ntpr = 100, ntwx = 100,
>
> ntt = 1, gamma_ln = 1.0,
>
> tempi = 300.0, temp0 = 300.0,
>
> nstlim = 1500000, dt = 0.001,
>
> cut = 12
>
> /
>
> I then run the following command -
>
> $AMBERHOME/exe/sander -O -i W43Y_GB_md1_rst.in -o W43Y_GB_md1_rst.out
> -c W43Y_GB_md1.rst -p W43Y.prmtop -r W43Y_GB_md1_rst.rst –x
> W43Y_GB_md1_rst.mdcrd
>
> The program exits very quickly and I get this in the tail of the
> output file (W43Y_GB_md1_rst.out) -
>
> --------------------------------------------------------------------------------
>
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
> rfree: End of file on unit 9
>
> If anyone could tell me what I'm doing wrong I'd appreciate it.
>
> thanks,
>
> John Love
>
> /*/John J. Love/*/
>
> /*/Chemistry and Biochemistry Department/*/
>
> /*/San Diego/*//*/ /*//*/State/*//*/ /*//*/University/*/
>
> /*/San Diego/*//*/, /*//*/CA/*//*/ /*//*/92182-1030/*/
>
> /*/619-594-2063/*/
>
> /http://www.chemistry.sdsu.edu/faculty/Love//
>

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