Thank Justin !
On Tue, Dec 18, 2012 at 7:20 AM, Justin Lemkul wrote:
>
>
> On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:
>
>> Dear All,
>>
>> When i do step EM, the output file .gro is separated into many step.pdb
>> files . And many errors "Water molecule starting at atom XXX can not be
>> sett
On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:
Dear All,
When i do step EM, the output file .gro is separated into many step.pdb
files . And many errors "Water molecule starting at atom XXX can not be
settled" appears. And the potential energy is positive !
What should i do to solve it ?
Pl
Sunny wrote:
Hi,
Continue to the energy minimization problem. I use l-bfgs to run the
energy minimization for the structure summarized in the previous message
below. The em output topology confout.gro doesn't contain velocity data.
Then, I try to convert confout.gro into .pdb format by:
As
Hi Sunny,
With energy minimization there are no velocities.
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
eorge
From: "Sunny" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error in Energy Minimization
Date: Tue, 16 Jan 2007 15:28:13 +
Hi Tsjerk,
The system has 1 protein (118 atoms) and 256 DPPC lipids (12800 at
-Protein : 12800 atoms
12 DPP : 12800 atoms
13 Other : 12800 atoms
George
From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "Discussion list for GROMACS users"
Subject: Re: [gmx-users] Error i
Hi George,
You didn't mention whether this was with or without solvent. This is
probably due to an error in your starting structure, and I advice to
check it carefully. Also, if you're running in solvent, check your
box.
Step= 57, Dmax= 4.3e-03 nm, Epot= -1.79963e+23 Fmax= inf, atom=
Sunny wrote:
Hi,
I have the following error when running energy minimization
(integrator=steep):
(similar message occurs serveral times in previous steps as for Step 57)
... ... ... ...
I'd like to know if there is any method to let this EM run.
Probably the problem is with your starting st
Hi,
I have the following error when running energy minimization
(integrator=steep):
(similar message occurs serveral times in previous steps as for Step 57)
... ... ... ...
Step 57, time 0.114 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 110.960770 (between atoms 1576 and
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