On 1/29/13 4:43 AM, SANTU BISWAS wrote:
dear users,
I am performing an energy minimization of
polypeptide(formed by 10-residues of alanine, lysine,leucine,glutamic
acid ) in vacuum box by using
Steepest Descent(initially) and then Conjugate Gradient methods in
gromacs_4.5.5_doub
and then MD.
Not sure about the energies. Maybe they should be negative ?
Andreas
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of Jussi Lehtola
> Sent: 14 May 2008 04:28
> To: Discussion list for GROMACS users
> Subject: RE:
silvester.thu
2008-05-14
发件人： Jussi Lehtola
发送时间： 2008-05-14 11:28:31
收件人： Discussion list for GROMACS users
抄送：
主题： RE: [gmx-users] Energy minimisation problem
On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
> On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wr
On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
> On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
> > First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if
> > it looks reasonable.
> >
> Thanks, using the vacuum method I seem to get better results.
It seems
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
> First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it
> looks reasonable.
>
> You could also have a look at the definition of ETHH in the GROMOS96
> forcefield, e.g. in ffG43a2.rtp. Although this is a united atom
.
Andreas
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of Jussi Lehtola
> Sent: 13 May 2008 11:36
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Energy minimisation problem
>
> Hi,
>
>
>
> I have constructed
Hi,
I have constructed topologies for methanol, ethanol, propanol and
butanol using x2top with the atomic coordinates from NIST Chemistry
WebBook. I have modified the topologies by putting the CH3s, CH2s and
OHs in their separate charge groups.
Now I have run into problems when trying to minimi
supti mukherjee wrote:
Dear all,
I was minimising a protein structure. I added polar hydrogens to the
protein by some program and then proceeded for the energy minimisation.
I chose Conjugate Gradient of 1000 steps with emtol as 100. The mdrun
came out with the following error.
" During neig
Dear all,
I was minimising a protein structure. I added polar hydrogens to the protein
by some program and then proceeded for the energy minimisation. I chose
Conjugate Gradient of 1000 steps with emtol as 100. The mdrun came out with
the following error.
" During neighborsearching, we assign each
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