@yahoo.com]
> Sent: Friday, April 05, 2013 5:22 PM
> To: Discussion list for GROMACS users
> Subject: Re: Fw: [gmx-users] water molecule can not be settled
>
> You mean start over the NPT step?
>
>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> Fr
water molecule can not be settled
You mean start over the NPT step?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, April 5, 2013 7:50 PM
Subject: Re: Fw: [gmx-users] water molecule can not be settled
On Fri, Apr 5, 2013 at
On Fri, Apr 5, 2013 at 11:22 AM, Shima Arasteh
wrote:
> You mean start over the NPT step?
>
>
Yes.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://w
You mean start over the NPT step?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, April 5, 2013 7:50 PM
Subject: Re: Fw: [gmx-users] water molecule can not be settled
On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
wrote:
> As I visualized the system, I see a water molecule somewhere between lipid
> chains near the protein entrance. This has been happen during NPT. I' d
> like to delete this molecule but with such a kind of fatal error this would
> impossible. S
ers] water molecule can not be settled
On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh
wrote:
I' d like to know if it is acceptable to change the molecule coordinates to
solve this problem?
>
>
It's unlikely that some ad hoc change will magically fix a problem. Energy
min
On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh
wrote:
> I' d like to know if it is acceptable to change the molecule coordinates
> to solve this problem?
>
>
It's unlikely that some ad hoc change will magically fix a problem. Energy
minimization should take care of clashes.
> Some time back, I
On Fri, Apr 5, 2013 at 9:55 AM, Shima Arasteh
wrote:
>
>
> Hi all,
>
> I am trying to simulate a system of protein and lipid bilayer ( in this
> case POPC). The ff I am using is CHARMM36 and I used related settings from
> literature.
>
> I used InflateGRO to pack the lipids around my protein. Then
ently. I really appreciate
your help.
Sincerely,
Shima
- Forwarded Message -
From: Shima Arasteh
To: Discussion list for GROMACS users
Sent: Friday, April 5, 2013 6:25 PM
Subject: [gmx-users] water molecule can not be settled
Hi all,
I am trying to simulate a system of protei
Hi all,
I am trying to simulate a system of protein and lipid bilayer ( in this case
POPC). The ff I am using is CHARMM36 and I used related settings from
literature.
I used InflateGRO to pack the lipids around my protein. Then put a position
restraint on my protein and P atoms of POPC. With
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
>
>
>
>
>
>
>
>
>
>
> - 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
>
>
>
>
>
>
>
> - 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
Robert Fenwick wrote:
Hi,
My simulation has fall over with this error:
t = 501.346 ps: Water molecule starting at atom 8367 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous
and current coordinates
What can I do to fix it? There are a few ot
Hi,
My simulation has fall over with this error:
t = 501.346 ps: Water molecule starting at atom 8367 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files
with previous
and current coordinates
What can I do to fix it? There are a few other that have had this
Hi Sunny,
The problem here is not the water. You have some serious problems with
your starting structure (which I already suspected from your previous
mails). It looks like your system has been very busy exploding, but
you never noticed because of the l-bfgs algorithm (controlled
explosion). Noti
Hi,
I have a structure with 1 protein (118 atoms), 256 DPPC lipids (12800
atoms), and 3833 water molecules (11499 atoms). The box size is 6.125, 12.5,
9.5 nm.
Water is add by genbox:genbox -cp input.pdb -cs spc216.gro -vdwd 0.45 -o
output.pdb
After the water added, I run the l-bfgs ene
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