On 9/24/12 4:57 PM, Lara Bunte wrote:
Hi
How to make the energy minimization in double precision? Do this mean to use
grompp twice?
No, you would have to recompile Gromacs in a different manner:
http://www.gromacs.org/Documentation/Terminology/Precision
I don't know if we have to go that
now a problem in the .mdp file.
Thanks for helping me
Greetings
Lara
- Ursprüngliche Message -
Von: Justin Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 18:34 Montag, 24.September 2012
Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
gt; >>> rvdw_switch = 0.8
> >>> rvdw= 1.5
> >>>
> >>> nstxout = 100
> >>> nstvout = 100
> >>> nstenergy = 100
> >>> nstlog = 100
> >>>
> >>> tcoupl
( :-(
Best greetings
Lara
- Ursprüngliche Message -
Von: Peter C. Lai
An: Lara Bunte
CC: "gmx-users@gromacs.org"
Gesendet: 17:57 Montag, 24.September 2012
Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
Then yes, your cutoffs are still wrong. However
= 300 300
> >
> > pcoupl = no
>
> I am totaly frustrated and shortly for giving it up :-(:-( :-(
>
> Best greetings
> Lara
>
>
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>
> - Ursprüngliche Message -
> Von: Peter C. Lai
>
. Lai
An: Discussion list for GROMACS users
CC: Lara Bunte
Gesendet: 22:13 Freitag, 21.September 2012
Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
>
>
> On 9/21/12 1:31 PM, Lara Bunte wrote:
> > Hi J
= 0.1 0.1
> ref_t = 300 300
>
> pcoupl = no
>
> Greetings
> Lara
>
>
>
>
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>
>
> - Ursprüngliche Message -
> Von: Peter C. Lai
> An: Lara Bunte
> CC: "gmx-users@gromacs.org"
> Gese
gt;
>
>
>
>
>
> - Ursprüngliche Message -
> Von: Peter C. Lai
> An: Lara Bunte
> CC: "gmx-users@gromacs.org"
> Gesendet: 17:46 Montag, 24.September 2012
> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
&
.September 2012
Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
Is this energy minimization or actual integrator = md?
On 2012-09-24 04:44:18PM +0100, Lara Bunte wrote:
> Hello
>
> Okay, I changed it to
>
> nstlist = 1
> rlist = 1.5
> r
r GROMACS users
> CC: Lara Bunte
> Gesendet: 22:13 Freitag, 21.September 2012
> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
>
> On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
> >
> >
> > On 9/21/12 1:31 PM, Lara Bunte wrote:
>
On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
>
>
> On 9/21/12 1:31 PM, Lara Bunte wrote:
> > Hi Justin
> >
> > I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and
> > with this settings grompp gives me two notes and one of this notes is
> > inconsistent:
> >
> > N
On 9/21/12 1:31 PM, Lara Bunte wrote:
Hi Justin
I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and with
this settings grompp gives me two notes and one of this notes is inconsistent:
NOTE 1 [file pr.mdp]:
For energy conservation with switch/shift potentials, rlist
tings
Lara
- Ursprüngliche Message -
Von: Justin Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 17:33 Freitag, 21.September 2012
Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
On 9/21/12 11:26 AM, Lara Bunte wrote:
> Hi Justin
>
> Sor
On 9/21/12 11:26 AM, Lara Bunte wrote:
Hi Justin
Sorry but I don't understand what you mean with "Despite being given the
correct settings for CHARMM27, you're still not using
them." I use exactly the settings Peter gave me in my last question. What is in
this settings wrong and where could
settings?
Greetings
Lara
- Ursprüngliche Message -
Von: Justin Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 16:04 Freitag, 21.September 2012
Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
On 9/21/12 9:45 AM, Lara Bunte w
On 9/21/12 9:45 AM, Lara Bunte wrote:
Hello
My equilibration of water around lumiflavin works (I got no error, no warning
and no note). Sadly the mdrun fails with following error:
step 886: Water molecule starting at atom 7596 can not be settled.
Check for bad contacts and/or reduce the time
Hello
My equilibration of water around lumiflavin works (I got no error, no warning
and no note). Sadly the mdrun fails with following error:
step 886: Water molecule starting at atom 7596 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
What does GROMACS me
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