Dear Jason Swails
thanks for your quick and useful replying. I did the mentioned steps for
md2.x file (adding iwrap=1), but the same error was printed out. The md2.x
file was pasted in the following. and is it possible to make a restart file
from this point if the md2.x file doesn't work? or I must do the simulation
from beginning?
Your Sincerely
S. Nasiri
=======================================================
equilibration for box
&cntrl
imin=0, ntpr=1000, ntwx=1000,
ntx=5, irest=1, iwrap=1,
tempi=298., temp0=298., ntt=3, cut=12,
gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1, nstlim=25000000,
ntwr=1000, dt=.001, ig=-1,
&end
===========================================================
cat md2.x
default_name
2258 0.9528000E+04
22.4789859 -6.9066054 27.7272280 25.9929062 9.8974097 5.2090811
12.7098467 30.8301582 8.0834424 3.8986970 -5.4171653 34.2276656
17.6735672 20.6086714 42.3992850 -4.3568596 -15.2958704 16.7112062
8.1036884 19.6802904 -10.5588697 3.4602180 19.0286650 11.2180001
23.5310144 36.1772211 -6.5295413 14.6121025 44.4954948 20.3309979
23.7046388 -3.6352530 41.3614238 33.1906999 -28.1669114 22.2645036
14.2471583 25.6602852 -2.6487804 18.0178470 4.8843151 30.0988887
41.2393182 -29.2255762 17.7753043 18.1913158 36.7135668 40.0457679
29.1689967 -12.4667223 -1.7658901 14.2860758 21.1798046 3.7351602
35.8992741 5.9006334 31.1361719 -22.8122607 -15.5383858 20.5248158
3.3237248 0.6503008 12.4768014 -21.3881875 13.5382728 1.1647585
62.6591762 62.6854028 5.2442720 62.2258913 62.4019786 6.1612759
62.2064644 63.5249852 4.6624499 62.4977867 61.8008204 4.6070079
64.0081602 63.0876431 5.5185463 64.3535274 63.1571403 4.6021141
49.3101377 -33.6707088 10.7911725 49.5245213 -32.8180570 11.4386544
48.6784643 -34.4978028 11.2623021 50.2542076 -34.2026706 10.4767773
48.6118374 -33.2640919 9.6636508 48.3407957 -34.0461600 9.1059971
-56.1464919 -12.9416519 37.9293181 -56.1254980 -13.4247963 38.9172229
-55.1479743 -12.5851661 37.7328086 -56.8681977 -12.0967753 37.8253557
-56.5420494 -13.8142671 36.9209983 -56.5599898 -13.4044620 35.9558956
64.9758088 78.0274498 0.5845363 65.5775587 78.4536234 1.3670532
63.9973273 78.5636506 0.5484273 64.8444747 76.9321015 0.8623669
65.6123688 78.0058414 -0.6823050 65.0020986 77.4586208 -1.2992278
-2.3626054 13.6159487 6.7563833 -1.7558630 12.9749091 7.4536335
-1.8096844 13.9510536 5.9112562 -2.7627302 14.4358646 7.2977209
-3.4758519 12.8974277 6.1716349 -3.2893196 11.9643149 5.7843469
2.1264291 -78.1092586 28.0529019 1.0789970 -77.8000573 28.0201904
2.1042899 -79.1910199 28.0573308 2.5089877 -77.5973844 29.0148975
2.8375788 -77.5394809 27.0090754 2.8506815 -76.5379270 27.1913966
39.2189511 24.3416789 -1.5710278 39.5316082 24.9862215 -0.7600483
38.0820893 24.4484635 -1.5902277 39.6092448 23.2807425 -1.3001337
39.8301763 24.7167201 -2.7536817 40.7906327 24.8881382 -2.5185146
-69.2625447 -33.1776189 -71.5160645 -69.5574087 -32.0828632 -71.7561985
-70.1396993 -33.6795851 -71.0771342 -68.3777118 -33.1177499 -70.8490067
-68.8585321 -33.8636595 -72.7418859 -68.6162257 -34.8078198 -72.5850001
-43.6451498 -18.0926970 43.4342307 -44.6706778 -18.2256831 43.1279503
-43.0269708 -17.7925453 42.5737139 -43.2344396 -19.0134615 43.8813099
-43.4876629 -17.1519356 44.5054312 -43.2522645 -17.6610889 45.3577137
-2.4402715 13.7026237 10.8706404 -3.1358331 14.0703060 10.0264217
-1.5316339 13.4931722 10.3511702 -2.7540886 12.6691258 11.1924698
-2.3214556 14.5271705 12.0187801 -3.0380305 14.4220232 12.7001284
-19.5600922 -31.0052432 -9.4652378 -19.2711300 -31.3710563 -10.3992166
-19.7065115 -31.7941486 -8.6835002 -20.4963479 -30.5073889 -9.6593548
-18.5705516 -30.0565986 -9.0606131 -17.8861805 -30.0642570 -9.7431397
-50.5993514 0.1877111 -15.6155492 -51.1018865 -0.7905194 -15.6463442
-49.4995145 0.0458611 -15.5781408 -50.9924339 0.6007044 -14.6531987
-51.0543986 1.0161510 -16.7338238 -51.9670761 1.3187967 -16.4770762
46.9671277 4.6900656 -37.2960024 48.0272038 4.5802488 -37.4467268
46.5605942 5.1946506 -38.1879851 46.6712655 5.2947890 -36.4294708
46.3943321 3.4160406 -37.2350649 46.1783063 3.1524917 -38.1292419
45.1619363 17.2690751 39.9912966 44.7446658 17.6399271 38.9980602
45.1075139 16.1688049 39.9851805 44.4478481 17.6118941 40.7750978
46.5094479 17.7438871 40.1827236 46.5064759 18.7642205 40.1025928
-3.1183345 14.6831498 -4.6327208 -2.6006906 13.8598976 -3.9722549
-2.4528874 15.5737487 -4.8909085 -4.0162814 15
==================================================================
cat md3.out
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| Run on 01/13/2014 at 09:37:17
[-O]verwriting output
File Assignments:
| MDIN: mdin.in
| MDOUT:
md3.out
|INPCRD:
md2.x
| PARM:
ionicbox.prmtop
|RESTRT:
md3.x
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
md3.dat
| MDCRD: md3.nc
|MDINFO:
mdinfo
| MTMD:
mtmd
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA:
inptraj
|
Here is the input file:
equilibration for
box
&cntrl
imin=0, ntpr=1000,
ntwx=1000,
ntx=5, irest=1,
iwrap=1,
tempi=298., temp0=298., ntt=3,
cut=12,
gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1,
nstlim=25000000,
ntwr=1000, dt=.001,
ig=-1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
peek_ewald_inpcrd: SHOULD NOT BE HERE
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 12 2014 - 23:00:03 PST
