Hi,
So what your system actually looks like is not clear, but if there are
more atoms than just residues 1 to 486 (that you;re calculating the
fluctuations for) then the 'rms first' commands may be doing *very*
different things in each run; since you didn't specify a mask for
either 'rms' command, they are using *all* atoms. If e.g. you have
multiple molecules in your system this can result in wildly different
reference structures as Carlos suggested.
-Dan
On Thu, Nov 4, 2021 at 8:30 PM 吴晓东 <18xdwu.stu.edu.cn> wrote:
>
> 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 Wed Dec 01 2021 - 08:30:04 PST
