VMD-L Mailing List

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Mon Apr 16 2018 - 10:43:25 CDT

Hi Peter,

Thanks for your reply on namd-I. I am sorry to post the same question here
without waiting for reply from namd-I.

Rabeta Yeasmin

On Sun, Apr 15, 2018 at 8:14 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> 1. Please see my reply on namd-l.
> 2. Please don't rapidly cross post between vmd-l and namd-l
>
> Thanks,
> Peter
>
> On Sun, Apr 15, 2018 at 7:57 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
> wrote:
>
>> Dear VMD Users,
>>
>> I have converted an all-atom lipid-protein system to a coarse-grained
>> system using residue based-coarse grained method (rbcg) where the protein
>> was at the center of the lipid. Later I did Steered MD simulation and
>> umbrella sampling simulation in the coarse-grained system. Now I want to
>> convert the last structure from my simulation to all-atom structure
>> (pdb file) where the protein is at 22A above the lipid. I was trying to do
>> it in VMD using reverse-rbcg model. But after running a while, it just
>> gets stuck. I had tried this several times and it has the same problem. I
>> am not sure what can be the problem.
>> Can you please suggest me what should I do?
>>
>> Thanks.
>>
>
>