Hi,Which tool(s) is/are useful? I don't have any idea for this problem.Thank you
you zou wrote:
> Hi again,
>
> Sorry, in "REMARK 470" there is:
>
> REMARK 470
>
> REMARK 470 MISSING ATOM
>
> REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
>
> REMARK 470 RES=RESIDUE N
On Mon, May 31, 2010 at 10:17 PM, wrote:
> Send gmx-users mailing list submissions to
>gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'hel
- Original Message -
From: Warren Gallin
Date: Tuesday, June 1, 2010 13:38
Subject: Re: [gmx-users] Constraint causing system to explode
To: Discussion list for GROMACS users
> Chris,
>
> As you suggested, I ran it on one node, and it still blew up,
> so it appears to be some odd
Chris,
As you suggested, I ran it on one node, and it still blew up, so it
appears to be some oddity with the constraint that I am imposing.
When I look at the dgdl.xvg file from the run, there appear to be a
number of transient spikes that are a couple orders of magnitude large
- Original Message -
From: Oleksandr
Date: Tuesday, June 1, 2010 12:43
Subject: Re: [gmx-users] water clusters MD
To: Discussion list for GROMACS users
> It would be helpful if you could be more specific. For example,
> the standard procedure described in tutorial:
>
> pdb2gmx -f input
It would be helpful if you could be more specific. For example, the standard
procedure described in tutorial:
pdb2gmx -f input.pdb
edit conf -f conf.gro d 0.5 -o newbox.gro
genbox -cp newbox.gro -cs spc2165.gro -p topol.top -o solvated.pdb
Now, could you please illustrate how would you do this f
- Original Message -
From: xho...@sohu.com
Date: Tuesday, June 1, 2010 11:53
Subject: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs
when using the ‘particle decomposition’ option.
To: gmx-users
> Hi, everyone of gmx-users,
>
> I met a problem when I use the ‘parti
- Original Message -
From: Nilesh Dhumal
Date: Tuesday, June 1, 2010 10:37
Subject: [gmx-users] vibrational spectra of glucose
To: gmx-users@gromacs.org
> Hello,
>
> I want to calculate the normal vibrational spectra of PF6 anion.
> After the energy minimization, I found that the struc
- Original Message -
From: Oleksandr
Date: Tuesday, June 1, 2010 11:39
Subject: Re: [gmx-users] water clusters MD
To: Discussion list for GROMACS users
> Look, in order to use editconf and gen box one need first to
> have gro and top files, which are generated by pdb2gmx. You say
You
Hi, everyone of gmx-users,
I met a problem when I use the ‘particle decomposition’ option in a NTP MD
simulation of Engrailed Homeodomain (En) in CL- neutralized water box. It just
crashed with an error “Fatal error in PMPI_Bcast: Other MPI error, error stack:
…..”. However, I’ve tried the ‘dom
Look, in order to use editconf and gen box one need first to have gro and top
files, which are generated by pdb2gmx. You say I don't need it. Ok may be
topology file can be written by hand, but what about "gro" file?
--- On Mon, 5/31/10, Mark Abraham wrote:
> From: Mark Abraham
> Subject: Re:
Hello,
I want to calculate the normal vibrational spectra of PF6 anion.
After the energy minimization, I found that the structure has lost his
symmetry. It does not have Oh symetry. I compared this structre with
ab-initio which is not matching.
I have pasted the input file for energy minimzatio
I've downloaded gromacs from the git repository. I type ./bootstrap
and get loads of warnings like this
configure.ac:414: warning: AC_CACHE_VAL(ac_m_cpu_7450, ...):
suspicious cache-id, must contain _cv_ to be cached
configure.ac:414: warning: AC_CACHE_VAL(ac_m_tune_970, ...):
suspicious cache-id,
you zou wrote:
Hi again,
Sorry, in "REMARK 470" there is:
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
Hi again,Sorry, in "REMARK 470" there is:REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE
MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES
Giovana Bergamini wrote:
Hi!
We have a problem with a protein-ligand-protein simulation. It is a somewhat
large system (approx. 360 amino acid residues with approx. 70 monosaccharides),
that requires a larger box for proper simulation.
We used exclusions (especifically for the problematic ato
>Hi!
>We have a problem with a protein-ligand-protein simulation. It is a somewhat
>large system (approx. 360 amino acid residues with approx. 70 monosaccharides),
>that requires a larger box for proper simulation.
>We used exclusions (especifically for the problematic atoms) and restrictions
>(t
On 5/31/10 6:21 PM, zhongjin wrote:
Dear users,
What's about the direction of Electric fields in GROMACS? For
example, E_z 1 0.01 5
means that the direction of Electric fields is along the +Z axis ? So
K+ will move along the +Z axis ?
E_z 1 -0.01 5 means that the direction of Electric fi
Dear users, What's about the direction of Electric fields in GROMACS? For
example, E_z 1 0.01 5means that the direction of Electric fields is along the
+Z axis ? So K+ will move along the +Z axis ?E_z 1 -0.01 5 means that the
direction of Electric fields is along the -Z axis ? So Cl- will
On 31.05.2010, at 17:37, grivet wrote:
> Le lundi 31 mai 2010 à 10:29 -0400, Justin A. Lemkul a écrit :
>>
>> Justin A. Lemkul wrote:
>>>
>>>
>>> grivet wrote:
Dear all,
I am running simulations of pure water at various temperatures. My first
step is an annealing from the
grivet wrote:
Le lundi 31 mai 2010 à 10:29 -0400, Justin A. Lemkul a écrit :
Justin A. Lemkul wrote:
grivet wrote:
Dear all,
I am running simulations of pure water at various temperatures. My first
step is an annealing from the previous temperature to the next one,
using a NPT ensemble. Us
Le lundi 31 mai 2010 à 10:29 -0400, Justin A. Lemkul a écrit :
>
> Justin A. Lemkul wrote:
> >
> >
> > grivet wrote:
> >> Dear all,
> >>
> >> I am running simulations of pure water at various temperatures. My first
> >> step is an annealing from the previous temperature to the next one,
> >> usi
On Mon, 2010-05-31 at 07:38 -0700, nanogroup wrote:
> Dear Justin,
>
> Let me tell the details:
>
> I have a PC with 4 CPU,
>
> Fedora 11 x86_64 is installed,
>
> The rpm files of Gromacs 4 are installed,
>
> now, I want to configure the gromacs to use all 4 CPUs,
>
> At the end of configurat
nanogroup wrote:
Dear Justin,
Let me tell the details:
I have a PC with 4 CPU,
Fedora 11 x86_64 is installed,
The rpm files of Gromacs 4 are installed,
now, I want to configure the gromacs to use all 4 CPUs,
At the end of configuration process, it says that the FFTW could not be
found!
Dear Justin,
Let me tell the details:
I have a PC with 4 CPU,
Fedora 11 x86_64 is installed,
The rpm files of Gromacs 4 are installed,
now, I want to configure the gromacs to use all 4 CPUs,
At the end of configuration process, it says that the FFTW could not be found!
The fftw files are ins
Justin A. Lemkul wrote:
grivet wrote:
Dear all,
I am running simulations of pure water at various temperatures. My first
step is an annealing from the previous temperature to the next one,
using a NPT ensemble. Using the result of that, I run an NVT simulation.
Where can I recover the box
grivet wrote:
Dear all,
I am running simulations of pure water at various temperatures. My first
step is an annealing from the previous temperature to the next one,
using a NPT ensemble. Using the result of that, I run an NVT simulation.
Where can I recover the box average box dimensions, vol
Dear all,
I am running simulations of pure water at various temperatures. My first
step is an annealing from the previous temperature to the next one,
using a NPT ensemble. Using the result of that, I run an NVT simulation.
Where can I recover the box average box dimensions, volume and density
of
- Original Message -
From: Oleksandr
Date: Monday, May 31, 2010 18:48
Subject: [gmx-users] water clusters MD
To: gmx-users@gromacs.org
> Hi,
> I'm new user of Gromacs. There are plenty examples how to do
> solvation study of various proteins. But I'd like to "solvate"
> highly ordered h
Hi,
I'm new user of Gromacs. There are plenty examples how to do solvation study of
various proteins. But I'd like to "solvate" highly ordered heavy water clusters
in box of light water. At the first step when I execute "pdb2gmx -f
watercluster.pdb" I get an error no matter which model is chose
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