Re: CGMD problem

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Wed Dec 03 2008 - 11:39:32 CST

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

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