Dear all,
I have a protein system that runs CMD in a water box with PBC. In this simulation, I looked at the trajectory file. The protein remained stable in the water box during the simulation process and did not run out of the water box. After running MD simulation, I want to analyze RMSF. I use the following input file to run with cpptraj.
#rmsf.in
parm prmtop
trajin S38D.nc
rms first
average crdset MyAvg
run
rms ref MyAvg
atomicfluct byres out S38D-old.rmsf :1-486.C,CA,N
Then, I want to see how RMSF will change if the protein is moved to the center of the water box. I wrote a wrap. In file and put the protein back in the center of the water box.
#wrap.in
parm prmtop
trajin S38D.nc
trajout wrap-S38D trajectory
image origin center familiar com :132
go
Based on the generated trajectory, I run the RMSF calculation again.
#rmsf-new.in
parm prmtop
trajin wrap-S38D
rms first
average crdset MyAvg
run
rms ref MyAvg
atomicfluct byres out S38D-old.rmsf :1-486.C,CA,N
It is puzzling that the protein is always in the water box whether it is moved to the center of the water box or not. So, I think the calculated RMSF should be consistent. However, the results of RMSF under these two conditions are very different. I don't know why?
The results are as follows：
①No moving protein：
#Res AtomicFlx
1.000 3.1073
2.000 2.9562
3.000 2.8570
4.000 2.9493
5.000 2.9838
6.000 3.0734
7.000 3.1263
8.000 3.1998
9.000 3.2446
10.000 3.2964
11.000 3.3608
12.000 3.4335
13.000 3.5786
14.000 3.5121
15.000 3.5382
16.000 3.5242
17.000 3.5047
18.000 3.6473
19.000 3.7766
20.000 3.9167
21.000 4.0491
22.000 4.2176
23.000 4.2456
24.000 4.0436
②Moving protein：
#Res AtomicFlx
1.000 1.7617
2.000 1.4648
3.000 1.1541
4.000 1.1855
5.000 1.0084
6.000 0.9336
7.000 0.9189
8.000 0.9765
9.000 1.0182
10.000 1.1047
11.000 1.2287
12.000 1.4049
13.000 1.4985
14.000 1.3945
15.000 1.3098
16.000 1.2191
17.000 1.1698
18.000 1.2880
19.000 1.4401
20.000 1.6805
21.000 1.9415
22.000 1.9977
23.000 1.9622
24.000 1.7602
It can be seen that the results are quite different, but I don't know why? In addition, can amber automatically handle periodic boundary conditions when calculating RMSF? When some residues of the protein run out of the water box, should I move the protein back to the center of the water box?
I really hope to get an answer.
Best,
Xiaodong
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Received on Sun Nov 07 2021 - 01:00:02 PST
