Re: CGMD problem

Date: Sat Dec 06 2008 - 14:30:39 CST

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.


(energy plot and conf files :

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
>> 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
>> 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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