Re: CGMD problem

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Sat Dec 06 2008 - 16:19:32 CST

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.
>>
>

-------------------------------------------------------------
The tree of liberty must be refreshed from time to time with the blood
of patriots and tyrants.

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