Just a first remark (more experience users and cpptraj specialists may
chime in here):
Perhaps cpptraj gets confused with the trajectory manipulation and the
analysis commands; you could try to separate these steps by using two
cpptraj-runs with two input files: in the first, you create a trajectory
with just the sytem your are interested in (and which is also easier to
inspect visually, including the respective distance), i.e. the centered
and imaged protein only; the the second, you do the actual distance
analysis.
For the first step, I'd also recommend to move all the strip commands in
your input file before the center and (more important) image commands;
this should considerably speed up execution.
In addition, if the image command fails for some reason - I guess you
have multiple chains in your system that "leave the box" during
simulation - and you used iwrap=1 in your MD input: you could try the
command unwrap in the first cpptraj run (-> strip, unwrap, center).
Maybe this helps.
Best regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 10.03.2022 um 08:45 schrieb chanyann06.stu.scu.edu.cn:
> Dear Amber Users，
>
> I carried out 2us GaMD of protein, which is composed of ten 200ns-MD trajectories. However, in the second trajectory, when I calculated distance between two residues, I got warnings as followed:
>
> ----- GaMDprod_02.nc (1-40000, 1) -----
>
> 0% 10% 20% 30% Warning: Frame 14529 imaging failed, box lengths are zero.
>
> Warning: Frame 14530 coords 1 & 2 overlap at origin; may be corrupt.
>
> Warning: Frame 14530 imaging failed, box lengths are zero.
>
> ……
>
> ……
>
> ……
>
> Warning: Frame 25099 coords 1 & 2 overlap at origin; may be corrupt.
>
> Warning: Frame 25099 imaging failed, box lengths are zero.
>
> 70% 80% 90% 100% Complete.
>
>
>
>
> Here is my .in file used to run the simulation:
>
> GaMD production
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ioutfm = 1,
> nstlim = 100000000,
> dt = 0.002,
> ntt = 3,
> gamma_ln = 5.0,
> ig = -1,
> tempi = 310.0,
> temp0 = 310.0,
> ntp = 0,
> ntb = 1,
> ntc = 2,
> ntf = 2,
> cut = 12,
> ntwr = 2500,
> ntpr = 2500,
> ntwx = 2500,
> ntwe = 2500,
> iwrap = 1,
> ntr = 0,
> ntwprt = 0,
>
> igamd = 3, iE = 1, irest_gamd = 1,
> ntcmd = 0, nteb = 0, ntave = 600000,
> ntcmdprep = 0, ntebprep = 0,
> sigma0P = 6.0, sigma0D = 6.0,
> &end
> /
>
>
>
> Here is the .in file I used to calculate the distance:
>
> parm step5_input.parm7
>
> trajin /home/xmpu233/cx/DAM128paraneo/GaMDprod_02.nc 1 last
>
> center origin :296-583
> image origin center
> strip :POPC
> strip :CHL1
> strip :SOD
> strip :CLA
> strip :WAT
> reference /home/xmpu233/cx/DAM128paraneo/step5_input.rst7
> distance :396.CA,C,O,N,H :510.CA,C,O,N,H out dis2.dat
>
>
> I have extracted a warning frame and found that all atom coordinates changes to zero, like this:
>
> CRYST1 0.000 0.000 0.000 0.00 0.00 0.00 1
> ATOM 1 N ARG 1 0.000 0.000 0.000 1.00 0.00 N
> ATOM 2 HT1 ARG 1 0.000 0.000 0.000 1.00 0.00 H
> ATOM 3 HT2 ARG 1 0.000 0.000 0.000 1.00 0.00 H
> ATOM 4 HT3 ARG 1 0.000 0.000 0.000 1.00 0.00 H
> ATOM 5 CA ARG 1 0.000 0.000 0.000 1.00 0.00 C
> ATOM 6 HA ARG 1 0.000 0.000 0.000 1.00 0.00 H
> ATOM 7 CB ARG 1 0.000 0.000 0.000 1.00 0.00 C
> ATOM 8 HB1 ARG 1 0.000 0.000 0.000 1.00 0.00 H
> ATOM 9 HB2 ARG 1 0.000 0.000 0.000 1.00 0.00 H
> ATOM 10 CG ARG 1 0.000 0.000 0.000 1.00 0.00 C
> ATOM 11 HG1 ARG 1 0.000 0.000 0.000 1.00 0.00 H
> ATOM 12 HG2 ARG 1 0.000 0.000 0.000 1.00 0.00 H
>
>
>
>
> "check" has been used in cpptraj to check the frame and I got this message:
>
> Warning: Unit cell size has changed so much that grid must be recalculated.
>
> Warning: Old sizes= {84, 84, 77} New sizes= {1, 1, 1}
>
> Warning: X cell offset reset to 1
>
> Warning: Y cell offset reset to 1
>
> Warning: Z cell offset reset to 1
>
> Total Grid memory: 0.208 kB
>
> terminate called after throwing an instance of 'std::bad_alloc'
>
> what(): std::bad_alloc
>
>
>
> It is confusing that the frames before and after the warning frames (14530-25099 frames report warnings) seem normal. Can the frame 14529 ( the one before warning) and frame 25100 (the one after warning) be continuous? What would cause this warning?
>
> I've check similar problems in amber mailing list but could not sovle it.
>
> Looking forward to your help and thanks a lot!
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 10 2022 - 01:00:02 PST
