Re: CGMD problem

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Sat Dec 06 2008 - 16:31:18 CST

Oh, wow, something really crazy is going on in that simulation :-).
Your bilayer and the protein move back and forth with huge amplitude.
Clearly, something is wrong, but I am not sure what. I would need to
look at all your files for this simulation and maybe try to run it
myself...

> I did do the minimization before the dynamics, and actually, it's
> also a little tricky to minimize the system including protein. To
> get rid of the message "Bad global exclusion count(possible error)"
> during the minimization, I need to increase the cutoff to 14.0,
> instead of using 12.0. However, this is not necessary for the system
> without protein (only membrane and water).
> Do you think this is reasonable?
I think it should be fine.

Maybe you could try to run an NVT simulation for a little while, to
let your system equilibrate, and then switch it to NVE? That may help,
although it's really strange anyway to see such a huge energy drift.

Anton.

On 6 Dec 2008, at 16:19, BIN ZHANG wrote:

> Hi, Anton:
>
> Thanks a lot for your quick response.
>
> You are right, the energy plot for the protein, is indeed for the
> the whole system.(sorry about the confusion). The trajectory does
> look quite peculiar actually, at least to me. It seems that the
> system is moving crazily, kind of falling apart (maybe exaggerated
> by the periodic wrapping). (I included a few rendered picture of the
> system here: http://www.its.caltech.edu/~bingo/ initial->mid1->mid2-
> >final).
>
> I did do the minimization before the dynamics, and actually, it's
> also a little tricky to minimize the system including protein. To
> get rid of the message "Bad global exclusion count(possible error)"
> during the minimization, I need to increase the cutoff to 14.0,
> instead of using 12.0. However, this is not necessary for the system
> without protein (only membrane and water).
> Do you think this is reasonable?
>
> Thanks a lot.
> Bin
>
>
>
> On Dec 6, 2008, at 1:45 PM, Anton Arkhipov wrote:
>
>> Hi Bin,
>>
>> No, I haven't encountered this problem before. Not sure what it can
>> be. The plot for the protein does indeed look strange.
>>
>> That plot for the protein, is it for the whole system (protein,
>> membrane, and water), or for the protein itself? Looks like you got
>> it from the NAMD log file, in which case it should be for the whole
>> system... How does the trajectory look? Anything strange you noticed?
>>
>> I'm not sure why you get this problem, but I would be glad to have
>> a look at all your file and at the trajectories for these
>> simulations. Maybe I could find something then. I will be on
>> travel, though, until Thursday. After that, I'll be happy to look
>> at your simulations, if you like.
>>
>> As a separate issue, why don't you minimize either of your systems?
>> Maybe you did it already before running these simulations...
>>
>> Best,
>>
>> Anton.
>>
>>
>>
>>
>>
>> On 6 Dec 2008, at 14:30, BIN ZHANG wrote:
>>
>>> Hi, Anton:
>>> Thanks a lot for your reference.
>>>
>>> To make sure the dynamics is running correctly, I just did 2
>>> NVE simulation, one including CG protein, CG membrane, and CG
>>> water(1st), and the other one includes only CG membrane and
>>> water(2nd).
>>>
>>> Then I found the energy of the 1st system is not
>>> conserved(please see the plot file cg_prot_ener.png), but the 2nd
>>> system does conserve energy(plot file cg_mem_ener.png).
>>>
>>> I just wonder whether you met this problem before? If not,
>>> then perhaps there might be something wrong with my protocol of
>>> coarse-graining the protein.
>>>
>>> Any suggestion is appreciated.
>>> Thanks a lot.
>>>
>>> Bin
>>>
>>> (energy plot and conf files : http://www.its.caltech.edu/~bingo/)
>>>
>>>
>>>
>>> On Dec 3, 2008, at 9:39 AM, Anton Arkhipov wrote:
>>>
>>>> Hi Bin,
>>>>
>>>> I would also like to point out the following. From the picture
>>>> you provided, it seems that you are trying to simulate a membrane
>>>> protein sitting in a membrane patch. Your protein has a well
>>>> defined tertiary structure, but the problem is that the RBCG
>>>> force-field is not good enough to maintain the tertiary structure
>>>> of proteins. If you want your protein to maintain its structure
>>>> during the RBCG simulation, you will need to add additional
>>>> "springs". Please see the following papers:
>>>>
>>>> Four-scale description of membrane sculpting by BAR domains.
>>>> Anton Arkhipov, Ying Yin, and Klaus Schulten. Biophysical
>>>> Journal, 95:2806-2821, 2008.
>>>>
>>>> Coarse-grained MD simulations of membrane protein-bilayer self-
>>>> assembly.
>>>> Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, Sansom MS.
>>>> Structure. 2008 Apr;16(4):621-30.
>>>>
>>>> This is just one more thing to keep in mind when using RBCG... As
>>>> to the lipid topology, that's like Peter said, we'll fix it in
>>>> the VMD cvs.
>>>>
>>>> Anton.
>>>>
>>>>
>>>>
>>>> On 2 Dec 2008, at 22:39, Peter Freddolino wrote:
>>>>
>>>>> Hi Bin,
>>>>>
>>>>> BIN ZHANG wrote:
>>>>>> Dear all:
>>>>>>
>>>>>> With many helps from people on the list, I now can run
>>>>>> the CGMD finally. Many thanks to you guys.
>>>>>>
>>>>>> But when I was checking the trajectory in VMD, a weird
>>>>>> cavity formed in my system, which is not supposed to happen.
>>>>>> The system was also going pretty wild( I attached one snapshot
>>>>>> of the system, water in bead rep, lipid and protein in bond rep)
>>>>>
>>>>> Even CG simulations can show unphysical behavior like voids if
>>>>> you don't equilibrate using a barostat... I believe that's what
>>>>> is happening here.
>>>>>
>>>>>> My questions are:
>>>>>> 1) I checked the CG POPC definition in the topology file and
>>>>>> found 12 beads are used(4 for each lipid tail, and the other 4
>>>>>> for lipid head). But if I remember correctly, the 2 lipid tails
>>>>>> in POPC has different number of carbons(1 with double bond has
>>>>>> 18, and another has 16). So can anyone explain why the exact
>>>>>> same beads
>>>>>> are used for 2 quite different tails?
>>>>> It looks like somewhere along the generations an error showed up
>>>>> in the distributed topology file. POPC's topology entry should be
>>>>> RESI POPC 0.00
>>>>> GROUP
>>>>> ATOM CHO Qo 0.70 ! Choline head group
>>>>> ATOM PHO Qa -0.70 ! Phosphate
>>>>> ATOM ES1 Na 0.00 ! Ester group
>>>>> ATOM ES2 Na 0.00 ! Ester group
>>>>> ATOM ME1 C 0.00 ! lipid tail
>>>>> ATOM ME2 C 0.00 ! lipid tail
>>>>> ATOM ME3 CDB 0.00 ! lipid tail double bond
>>>>> ATOM ME4 C 0.00 ! lipid tail
>>>>> ATOM MT1 C 0.00 ! lipid tail terminus
>>>>> ATOM ME5 C 0.00 ! lipid tail
>>>>> ATOM ME6 C 0.00 ! lipid tail
>>>>> ATOM ME7 C 0.00 ! lipid tail
>>>>> ATOM MT2 C 0.00 ! lipid tail terminus
>>>>> BOND CHO PHO PHO ES1 ES1 ES2 ES1 ME1
>>>>> BOND ME1 ME2 ME2 ME3 ME3 ME4 ME4 MT1
>>>>> BOND ES2 ME5 ME5 ME6 ME6 ME7 ME7 MT2
>>>>>
>>>>> I'll make sure the correct entry is added to the vmd cvs; not
>>>>> sure how that crept in there.
>>>>>> 2) Since I got the error "Unable to find angle parameter for
>>>>>> Nxg Nxx Nxg" when the simulation was started, I added the
>>>>>> following parameters into the CG parameter file:
>>>>>> Nxg Nxx Nxg 2.988 92
>>>>>> Nxg Nxg Nxg 2.988 92
>>>>>> Is this reasonable?
>>>>> Looks fine.
>>>>> Best,
>>>>> Peter
>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------------
>>> The tree of liberty must be refreshed from time to time with the
>>> blood of patriots and tyrants.
>>>
>>
>
>
>
>
>
>
>
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>
> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the
> blood of patriots and tyrants.
>

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