Hello everyone,
I am using Amber11 for MD
simulation. It works nice but when run a segment for 20ns ( that is 5000 snapshots) at a time, I got problem with the last several snapshots in the output dcd file. Taking the rmsd of the protein backbone for example it is about 230A while the normal ones are around 3A.
I use ptraj
from amber11 for rmsd calculation and it works well with other snapshots
except with the ones form 40280-40460 ps and 60280-60460 ps that are
the final 70 snapshots of npt13.dcd and npt14.dcd both the input and
output are attached behind.
By the way, the output energy temperature density pressure and volume are fine ...
So what can we do to further finger out the problem and please let me know if you need other information to help
Thanks very much
input;
trajin ../pro-lig-mw-Na6-Cl73-nve-npt8.binpos 1 230
2
trajin ../pro-lig-mw-Na6-Cl73-npt9.dcd.gz 1 500 1
trajin ../pro-lig-mw-Na6-Cl73-npt11.dcd.gz 1 2000 1
trajin ../lig-pro-npt12.dcd.gz 1 2500 1
trajin ../lig-pro-npt13.dcd 1
5000 1
trajin ../lig-pro-npt14.dcd 1 5000 1
center :1-204 mass origin
image origin center familiar
(also tried
center .CA mass origin
image origin center
but no luck)
rms first out pro-lig-bb.rms :
1-204.CA,C,N time 4.0
rms first out
pro-lig-all.rms :1-204 time 4.0
rms first out trp-a.rms :102 time 4.0
rms first out trp-c.rms
:204 time 4.0
rms first out pro-lig-ABC-bb.rms :9-24,28-35,
38-56.CA,C,N time 4.0
rms first out pro-lig-ABC-all.rms :9-24,28-35,38-56 time 4.0
rms first out pro-lig-A2B2C2-bb.rms :111-126,130-137,
140-158.CA,C,N time
4.0
rms first out pro-lig-A2B2C2-all.rms :111-126,130-137,140-158 time 4.0
rms first out pro-lig-DE-bb.rms :61-68,
72-85.CA,C,N time 4.0
rms first out pro-lig-DE-all.rms :61-68,72-85 time 4.0
rms first out pro-lig-D2E2-bb.rms
:163-170,
174-187.CA,C,N time 4.0
rms first out pro-lig-D2E2-all.rms :163-170,174-187 time 4.0
rms
first out pro-lig-ABCA2B2C2-bb.rms
:9-24,28-35,38-56,111-126,130-137,
140-158.CA,C,N time
4.0
rms first out pro-lig-ABCA2B2C2-all.rms
:9-24,28-35,38-56,111-126,130-137,140-158 time 4.0
rms first out pro-lig-DED2E2-bb.rms :61-68,72-85,163-170,
174-187.CA,C,N time 4.0
rms first out pro-lig-DED2E2.rms :61-68,72-85,163-170,174-187 time 4.0
the output is like this:
40196.00 3.62379
40200.00 3.57787
40204.00
3.59396
40208.00 3.55176
40212.00 3.55755
40216.00 3.61072
40220.00 3.51690
40224.00 3.54457
40228.00 3.50856
40232.00 3.56595
40236.00 3.53495
40240.00 3.58373
40244.00 3.56591
40248.00 3.55274
40252.00 3.56384
40256.00 3.53552
40260.00 3.48354
40264.00 3.51672
40268.00 3.51680
40272.00 3.53946
40276.00 3.57942
40280.00 503.47216
40284.00 494.06059
40288.00 495.91581
40292.00 500.73311
40296.00 499.34041
40300.00 500.75827
40304.00 501.74491
40308.00 496.50253
40312.00 495.08027
40316.00
505.68574
40320.00 494.19087
40324.00 498.10471
40328.00 503.00141
40332.00 497.00654
40336.00 501.32159
40340.00 496.44208
40344.00 495.67839
40348.00 494.64808
40352.00 504.41720
40356.00 498.79969
40360.00 501.37176
40364.00 502.52509
40368.00 493.50986
40372.00 509.02993
40376.00 496.07358
40380.00 493.26818
40384.00 514.88252
40388.00 499.15561
40392.00 500.30938
40396.00 495.32700
40400.00 499.57580
40404.00 491.11505
40408.00 496.33841
40412.00 501.97969
40416.00 500.34191
40420.00 496.52573
40424.00 504.95763
40428.00 503.96328
40432.00 500.79367
40436.00 499.56972
40440.00 497.96784
40444.00 500.37400
40448.00 502.83966
40452.00
490.74727
40456.00 490.13810
40460.00 501.93728
40464.00 3.43600
40468.00 3.40314
40472.00 3.42939
40476.00 3.47919
40480.00 3.45434
40484.00 3.47105
40488.00 3.40627
40492.00 3.41956
40496.00 3.37335
40500.00 3.39285
40504.00 3.43147
40508.00 3.40280
40512.00 3.38379
.
.
.
.
60208.00 3.49698
60212.00 3.49558
60216.00 3.40186
60220.00 3.37891
60224.00 3.31956
60228.00 3.33794
60232.00 3.40359
60236.00 3.38580
60240.00 3.37928
60244.00
3.33913
60248.00 3.39330
60252.00 3.32382
60256.00 3.33229
60260.00 3.37229
60264.00 3.39414
60268.00 3.43121
60272.00 3.50082
60276.00 3.48373
60280.00 495.36233
60284.00 490.47826
60288.00 502.35940
60292.00 496.09247
60296.00 497.86649
60300.00 502.86591
60304.00 504.75363
60308.00 499.00816
60312.00 494.89123
60316.00 491.34819
60320.00 498.31413
60324.00 488.01539
60328.00 492.81843
60332.00 503.94241
60336.00 499.65280
60340.00 495.46360
60344.00 493.57554
60348.00 498.60472
60352.00 510.43223
60356.00 496.53787
60360.00 498.32477
60364.00 484.86662
60368.00
495.70181
60372.00 502.42476
60376.00 497.43111
60380.00 501.62143
60384.00 497.66322
60388.00 494.27478
60392.00 495.69731
60396.00 502.94928
60400.00 497.97454
60404.00 499.91530
60408.00 506.37999
60412.00 495.24463
60316.00 491.34819
60320.00 498.31413
60324.00 488.01539
60328.00 492.81843
60332.00 503.94241
60336.00 499.65280
60340.00 495.46360
60344.00 493.57554
60348.00 498.60472
60352.00 510.43223
60356.00 496.53787
60360.00 498.32477
60364.00 484.86662
60368.00 495.70181
60372.00 502.42476
60376.00 497.43111
60380.00 501.62143
60384.00 497.66322
60388.00 494.27478
60392.00 495.69731
60396.00 502.94928
60400.00 497.97454
60404.00
499.91530
60408.00 506.37999
60412.00 495.24463
60416.00 505.38098
60420.00 512.19207
60424.00 495.53304
60428.00 497.23037
60432.00 490.11806
60436.00 491.99509
60440.00 502.54092
60444.00 499.06300
60448.00 503.49534
60452.00 502.92540
60456.00 504.16717
60460.00 500.31077
--- 11年1月10日，周一, xueqin pang <pangxueqintea.yahoo.com.cn> 写道：
发件人: xueqin pang <pangxueqintea.yahoo.com.cn>
主题: Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2011年1月10日,周一,下午11:08
--- 11年1月10日，周一, case <case.biomaps.rutgers.edu> 写道：
发件人: case <case.biomaps.rutgers.edu>
主题: Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2011年1月10日,周一,下午10:05
On Mon, Jan 10, 2011, xueqin pang wrote:
>
> I am using Amber11 for MD
simulation. It works nice but when
> run a segment for 20ns ( that is 5000 snapshots) at a time, I got
> problem with the last several snapshots in the output dcd file. Taking
> the rmsd of the protein backbone for example it is about 230A while
You need to say exactly how you computed the rmsd. This is probably a simple
matter of making sure you are correctly reading the box information from the
trajectory file, but without even know what program you are using (much less
what input) we can't help much.
...dac
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Received on Tue Jan 11 2011 - 08:30:07 PST
