It depending the time steps that u used or the molecule that u had is
big..Thats why ur EM take a long time..Is better take a long time
rather than quick but had a lot of errors..
On Wed, Oct 23, 2013 at 9:59 AM, Nimmy McNimmerson [via GROMACS]
wrote:
> I have some simulations of inserting a prob
Thanks Justin for the quick reply.
by the way after i solvated the protein with water and i change the
amount of the protein that i want for example 8 and the amount of
water that already in is 20453.But after i proceed with grompp the
result shows that my .top file have different number of config
Hi Eric,
I'm using gromacs 4.5.5.
Is it the version is different for dssp?
Thanks
On Fri, Jun 7, 2013 at 3:41 AM, Erik Marklund [via GROMACS]
wrote:
> HI,
>
> What version of gromacs is this? DSSP changed its syntax a while back and we
> had to adjust do_dssp accordingly. You may have a mismatc
Hi Maggin,
It depend on your protein stability..It can be short or long..Check
the .edr file by using g_energy
On Thu, May 23, 2013 at 9:44 AM, maggin [via GROMACS]
wrote:
> Hi, when simulation small peptideS, 6 or 10 amino acid, how long it is need
> for NVT and NPT?
>
> ___
Thanks Dr. Dallas for your replying.
But my friend told me that the extended one is only 2 ns not the total 22ns.
So,the gro for the extended one is not affect at all?
I thought that the gro file that prodice from the extend one is only 2 ns.
Thanks Doc!
On Wed, Mar 13, 2013 at 11:19 AM, Dalla
minimize -v
Need to edit the em1.mdp by using the highest emtol starting from 1000
and decrease it little by little to get the lowest energy.
Regards,
SHika
On Tue, Oct 23, 2012 at 11:14 AM, Nur Syafiqah Abdul Ghani
wrote:
> Okay thanks for the explanation Justin.
>
> But,i would like t
twice
On Mon, Oct 8, 2012 at 9:21 AM, Justin Lemkul [via GROMACS]
wrote:
>
>
> On 10/7/12 9:17 PM, shika wrote:
>
>> Thanks Justin.
>>
>> May I ask something, if i'm using the command for genbox before
>> minimization which is
>>
>> genbox
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