Re: [gmx-users] Re: the number of water molecules (Jian Zou)

[Erik Marklund]

Now, did you try searching the mailing lists before asking this? This
question pops up once a week or so. Check the archives: the truth is out
there.

/Erik

Dechang Li skrev:
>> Message: 2
>> Date: Mon, 21 Apr 2008 10:43:27 -0400
>> From: "Jian Zou" <[EMAIL PROTECTED]>
>> Subject: [gmx-users] Re: the number of water molecules
>> To: gmx-users@gromacs.org
>> Message-ID:
>>  <[EMAIL PROTECTED]>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> How about using vmd selection "within" to do this
>> 
>
>  I have tried this. However, vmd can tell me the number in this
> frame, but there are about 5000 frames! I am tring to write a script
> to let vmd explore the results to a file VS. frames. If I make 
> any progress, let you know. ^_^
>
>
>   
>>>  Message: 3
>>>  Date: Sun, 20 Apr 2008 21:01:57 +0800
>>>  From: Dechang Li <[EMAIL PROTECTED]>
>>>  Subject: [gmx-users] the number of water molecules
>>>  To: "gmx-users" 
>>>  Message-ID: <[EMAIL PROTECTED]>
>>>  Content-Type: text/plain;   charset="gb2312"
>>>
>>>  Dear all,
>>>
>>> How can I calculate the number of water molecules around the
>>>  protein with a distance about 5 angstrom? Is that possible in
>>>  Gromacs?
>>>
>>>
>>>
>>>  Best regards,
>>>
>>>  2008-4-20
>>>
>>>
>>>  =
>>>  Dechang Li, PhD Candidate
>>>  Department of Engineering Mechanics
>>>  Tsinghua University
>>>  Beijing 100084
>>>  PR China
>>>
>>>  Tel:   +86-10-62773779(O)
>>>  Email: [EMAIL PROTECTED]
>>>  =
>>>
>>>   
>> --
>> 
>
>
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-- 
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
[EMAIL PROTECTED]http://xray.bmc.uu.se/molbiophys

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[gmx-users] Re: ice box contact water box

[Mark Abraham]

Wei, Xiupeng wrote:

Hi Mark,
  Could you give me some suggestions for how to put two boxes 
contacting each other? Thanks.

Best regards,
xiupeng

Dear Vasilii and other users,
  Thanks for you reply.
  I triedto do the simulation you said.   But how to setup the initial 
configuration which is putting water contacting with ice, I knew in Gms tutor 
there is a example of mixed water and mathenol, it is a water box contacting 
with a mathenol box. I searched mailing list and wikki, however, no useful 
information to create such a configuration. Would you give me some suggestions?
 Does it still use editconf and genbox to create it?


Please leave GROMACS-related questions on the emailing list so that all 
can learn from the answers, and the answers can be found in the archives.


If you already have a box of ice, then genbox can fill the rest with 
water, once you play around with the box dimensions to create space for 
it to fill. You're on your own for making a box of ice, however - search 
the web and the literature.


Mark
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Re: [gmx-users] water can't freeze

[Erik Marklund]

I think you'll have to do it manually. The geometry for ice shouldn't be 
too hard to find, and with that you can build your own coordinate file 
for a chunk of ice. Ice is not the only nucleating agent for water 
freezing though. In large scale nucleation protocols some silver 
compound is used if I remember correctly. Still, nucleation reactions 
are generally pretty slow in comparison to melting, so don't expect to 
see much happening in the first hundreds of ps.


/Erik

Wei, Xiupeng skrev:

Dear Vasilii and other users,
  Thanks for you reply.
  I triedto do the simulation you said.   But how to setup the initial 
configuration which is putting water contacting with ice, I knew in Gms tutor 
there is a example of mixed water and mathenol, it is a water box contacting 
with a mathenol box. I searched mailing list and wikki, however, no useful 
information to create such a configuration. Would you give me some suggestions?
 Does it still use editconf and genbox to create it?

Best regards,
xiupeng

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Vasilii Artyukhov [EMAIL 
PROTECTED]
Sent: Saturday, April 19, 2008 12:17 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] water can't freeze

Dear Xiupeng,

What you're seeing is the difference between freezing water and overcooling it. 
If you want your water to crystallize, you'll actually have to make it - e.g., 
by putting it in contact with ice. Normally, pure water doesn't freeze on its 
own, you can easily verify this experimentally at home :)

Best regards,
Vasilii

2008/4/19, Wei, Xiupeng <[EMAIL PROTECTED]>:
Hi gmx users,
 I'm a new Gromacs user. Till now, I can get pretty good simulation of 
ice melting to water, but why can't I simulate water freezing to ice?
 The .top and .gro files used for water freezing simulation are 
generated by ice melting to 310K. I changed the temperature in .mdp file to 
230K, but after mdrun, the water was still water, it can't freeze?
 How can I get water freezing to ice?
I paste mdp for your reference.
Thanks.

best,
xiupeng


title= icing at 230 K with cuffoff
cpp  = /lib/cpp
integrator   = md
;Time step
dt   = 0.002
nsteps   = 10
;Output control
nstxout  = 10
nstvout  = 10
nstlog   = 100
nstenergy= 100
nstxtcout= 100
;Neigbour searching
nstlist  = 10
ns_type  = grid
rlist= 0.8
;Non bonded interaction
coulombtype  = pme
optimize_fft = yes
fourierspacing   = 0.2
pme-order= 6
ewald-rtol   = 1e-05
rcoulomb = 0.8
vdw-type = Cut-off
rvdw = 0.8
DispCorr = EnerPres
;Temperature coupling
tcoupl   = berendsen
tc-grps  = System
tau_t= 0.1
ref_t= 230
;Pressure coupling
pcoupl   = berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 5e-5
ref_p= 1.0

gen_temp = 230.0
constraints  = all-bonds
; generate velocities
gen_vel  = yes
gen_seed = 173529


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--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
[EMAIL PROTECTED]http://xray.bmc.uu.se/molbiophys

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Re: [gmx-users] Loop displacement calculation?

[Mark Abraham]

SeungPyo Hong wrote:

Thank you for your kind response.

I think that I do not clearly describe the system.

The loop I mentioned above seems to interact with the other parts of the 
protein with hydrophobic interactions.
So, the displacement of the loop from the original position will make 
the free energy difference, and this can estimate the energy stabilized 
by the loop placement on its natural form.


Is this statement seems to be reasonable?


That makes a lot more sense, however I don't have the expertise to judge 
whether there's a better method around.


Frankly I am not understanding the free energy calculation method, and 
maybe it is the reason why I think that this simulation works.
I premised that if the free energy code really calculate the free energy 
a certain ensenble of microstates, it can be used to test the stability 
of the part of the protein.


Follow the links here 
http://wiki.gromacs.org/index.php/Special:Search?search=free+energy&go=Go 
for some tutorial material. Obviously, you will only ever calculate free 
energy *differences*.


Mark
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Re: [gmx-users] water can't freeze

[Ran Friedman]

There are several different crystal phases of water. For simulation
setup, it's best (always, not only with freezing of water) to check the
literature. This will also give you a hint on what have already been
done. Quite a few MD simulations of ice were reported. If you have a
good idea on what you want to see, verify that it hasn't already been
performed.

Ran.

Erik Marklund wrote:
> I think you'll have to do it manually. The geometry for ice shouldn't
> be too hard to find, and with that you can build your own coordinate
> file for a chunk of ice. Ice is not the only nucleating agent for
> water freezing though. In large scale nucleation protocols some silver
> compound is used if I remember correctly. Still, nucleation reactions
> are generally pretty slow in comparison to melting, so don't expect to
> see much happening in the first hundreds of ps.
>
> /Erik
>
> Wei, Xiupeng skrev:
>> Dear Vasilii and other users,
>>   Thanks for you reply.
>>   I triedto do the simulation you said.   But how to setup
>> the initial configuration which is putting water contacting with ice,
>> I knew in Gms tutor there is a example of mixed water and mathenol,
>> it is a water box contacting with a mathenol box. I searched mailing
>> list and wikki, however, no useful information to create such a
>> configuration. Would you give me some suggestions?
>>  Does it still use editconf and genbox to create it?
>>
>> Best regards,
>> xiupeng
>> 
>> From: [EMAIL PROTECTED] [EMAIL PROTECTED]
>> On Behalf Of Vasilii Artyukhov [EMAIL PROTECTED]
>> Sent: Saturday, April 19, 2008 12:17 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] water can't freeze
>>
>> Dear Xiupeng,
>>
>> What you're seeing is the difference between freezing water and
>> overcooling it. If you want your water to crystallize, you'll
>> actually have to make it - e.g., by putting it in contact with ice.
>> Normally, pure water doesn't freeze on its own, you can easily verify
>> this experimentally at home :)
>>
>> Best regards,
>> Vasilii
>>
>> 2008/4/19, Wei, Xiupeng
>> <[EMAIL PROTECTED]>:
>> Hi gmx users,
>>  I'm a new Gromacs user. Till now, I can get pretty good
>> simulation of ice melting to water, but why can't I simulate water
>> freezing to ice?
>>  The .top and .gro files used for water freezing simulation
>> are generated by ice melting to 310K. I changed the temperature in
>> .mdp file to 230K, but after mdrun, the water was still water, it
>> can't freeze?
>>  How can I get water freezing to ice?
>> I paste mdp for your reference.
>> Thanks.
>>
>> best,
>> xiupeng
>>
>>
>> title= icing at 230 K with cuffoff
>> cpp  = /lib/cpp
>> integrator   = md
>> ;Time step
>> dt   = 0.002
>> nsteps   = 10
>> ;Output control
>> nstxout  = 10
>> nstvout  = 10
>> nstlog   = 100
>> nstenergy= 100
>> nstxtcout= 100
>> ;Neigbour searching
>> nstlist  = 10
>> ns_type  = grid
>> rlist= 0.8
>> ;Non bonded interaction
>> coulombtype  = pme
>> optimize_fft = yes
>> fourierspacing   = 0.2
>> pme-order= 6
>> ewald-rtol   = 1e-05
>> rcoulomb = 0.8
>> vdw-type = Cut-off
>> rvdw = 0.8
>> DispCorr = EnerPres
>> ;Temperature coupling
>> tcoupl   = berendsen
>> tc-grps  = System
>> tau_t= 0.1
>> ref_t= 230
>> ;Pressure coupling
>> pcoupl   = berendsen
>> pcoupltype   = isotropic
>> tau_p= 1.0
>> compressibility  = 5e-5
>> ref_p= 1.0
>>
>> gen_temp = 230.0
>> constraints  = all-bonds
>> ; generate velocities
>> gen_vel  = yes
>> gen_seed = 173529
>>
>>
>> ___
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Re: [gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

[Marc F. Lensink]

On Mon, Apr 21, 2008 at 07:09:31PM +0400, Vasilii Artyukhov wrote:
> Dear GROMACS users,
> 
> particularly, those experienced with membrane simulations,
> 
> I want to simulate lipid bilayers (e.g., DPPC) in the presence of certain
> small solutes, much like what was done in A.K. Sum & J.J. de Pablo, Biophys.
> J. 85, 3636 (2003) with DMSO. I'd like to use the TIP5P and OPLS all-atom
> parameters for water and other stuff, but there's still the question of what
> parameters to use for lipids. I'm aware that I'm supposed to do my own
> research on this matter, but it'd still be very nice to have some advice on
> the choice of parameters from someone with more experience in these things.

i'm very happily using berger/oplsaa/tip4p.  mind that this means ua
lipid tails and the rest aa, so unless you have a distinct lipid
phase, it's probably not what you want.  personally i'm not (yet)
convinced it's a better combination than berger/gromos/spc, though.

cheers,
marc


-- 
Marc F. Lensink
Centre for Structural Biology and Bioinformatics  CSBB
Université Libre de Bruxelles   [EMAIL PROTECTED]
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425
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Re: [gmx-users] x2top error in CNT simulation

[David van der Spoel]

Hero wrote:

Dear All,

I am trying to simulate water flow in CNT and just followed the website:
http://cs86.com/CNSE/SWNT.htm

I did the following:

1. ffgmx.n2t
 must change this files name to ffencadv.n2t and add the following 2 lines:
C C 1 C ; CNT Carbon with one bond
C C 2 C C ; CNT double bonded Carbon

2. ffgmxbon.itp
add the following line to it:

#
[ bondtypes ]
; i j func b0 kb
C C 1 0.14210 478900.
#
[ angletypes ]
; i j k func th0 cth
C C C 1 120.000 397.480
#
[ dihedraltypes ]
; i l func q0 cq
C C 1 0.000 167.360
#

But when I ran:
x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

Error message appeared:

Can not find forcefield for atom C-143 with 2 bonds
Can not find forcefield for atom C-144 with 2 bonds

---
Program x2top, VERSION 3.3.3
Source code file: x2top.c, line: 206

Fatal error:
Could only find a forcefield type for 0 out of 144 atoms
---
Could you please tell me what is the problem?


x2top -pbc
where are these atoms, on the edge of the CNT? Is your box size correct 
such that you have a periodic CNT?






Thank you very much!

Jue


  

Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] grompp error, invalid line in .gro file

[Andreas Kring]

Hello all.

I'm trying to simulate an argon liquid. The OPLS-AA force field is used 
with the files from /usr/local/gromacs/share/gromacs/top. But I get an 
error when I run


$ grompp -f NVT.mdp -c Ar.gro -p Ar.top
---
Program grompp, VERSION 3.3.3
Source code file: confio.c, line: 709

Fatal error:
Invalid line in Ar.gro for atom 1:
1Argon Ar 1 0.0 0.0 0.0
---

An ideas on what can be wrong? My argon .top file and .gro file can be 
seen below.


Kind regards
Andreas

--
Ar.top
--
; Topology file for Ar

; Parameter level

#include "ffoplsaa.itp"
;#define _FF_OPLS
;#define _FF_OPLSAA
;[defaults]
;#include "ffoplsaanb.itp"
;   [atomtypes]
;#include "ffoplsaabon.itp"
;   [bondtypes]
;   [constrainttypes]
;   [angletypes]
;   [dihedraltypes]

; Molecule level

[ moleculetype ]
; molname   nrexcl
Argon   1

[ atoms ]
; idat_type res_nr  res_nameat_name cg_nr   charge
1   opls_0971   Argon   Ar  1   0.0

; System level

[ system ]
Argon liquid

[ molecules ]
Argon 2048

-
Ar.gro
-
fcc lattice of argon atoms
2048
1Argon Ar 1 0.0 0.0 0.0
2Argon Ar 2 0.283835 0.283835 0.0
...
2047Argon Ar 2047 4.257525 3.97369 4.257525
2048Argon Ar 2048 3.97369 4.257525 4.257525
4.54136 4.54136 4.54136

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Re: [gmx-users] grompp error, invalid line in .gro file

[Justin A. Lemkul]

Just thinking out loud, but maybe "Argon" is too long of a name for the
residues.  The longest I think I've seen is 4 characters (something like LYSH
or ARGN, for example).  Maybe the length of the name is throwing off the
formatting.  Why don't you try again with a residue name of something like AR
(in both the .top and .gro, of course) and see if that fixes things.

-Justin

Quoting Andreas Kring <[EMAIL PROTECTED]>:

> Hello all.
>
> I'm trying to simulate an argon liquid. The OPLS-AA force field is used
> with the files from /usr/local/gromacs/share/gromacs/top. But I get an
> error when I run
>
> $ grompp -f NVT.mdp -c Ar.gro -p Ar.top
> ---
> Program grompp, VERSION 3.3.3
> Source code file: confio.c, line: 709
>
> Fatal error:
> Invalid line in Ar.gro for atom 1:
> 1Argon Ar 1 0.0 0.0 0.0
> ---
>
> An ideas on what can be wrong? My argon .top file and .gro file can be
> seen below.
>
> Kind regards
> Andreas
>
> --
> Ar.top
> --
> ; Topology file for Ar
>
> ; Parameter level
>
> #include "ffoplsaa.itp"
> ;#define _FF_OPLS
> ;#define _FF_OPLSAA
> ;[defaults]
> ;#include "ffoplsaanb.itp"
> ;   [atomtypes]
> ;#include "ffoplsaabon.itp"
> ;   [bondtypes]
> ;   [constrainttypes]
> ;   [angletypes]
> ;   [dihedraltypes]
>
> ; Molecule level
>
> [ moleculetype ]
> ; molname nrexcl
> Argon 1
>
> [ atoms ]
> ; id  at_type res_nr  res_nameat_name cg_nr   charge
> 1 opls_0971   Argon   Ar  1   0.0
>
> ; System level
>
> [ system ]
> Argon liquid
>
> [ molecules ]
> Argon 2048
>
> -
> Ar.gro
> -
> fcc lattice of argon atoms
> 2048
> 1Argon Ar 1 0.0 0.0 0.0
> 2Argon Ar 2 0.283835 0.283835 0.0
> ...
> 2047Argon Ar 2047 4.257525 3.97369 4.257525
> 2048Argon Ar 2048 3.97369 4.257525 4.257525
> 4.54136 4.54136 4.54136
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
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>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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[gmx-users] Re: gmx-users Digest, Vol 48, Issue 67

[Jian Zou]

set sel [atomselect $molid "selection"]

for {set iframe 0} {$iframe < $nframe} {incr iframe} {
$sel frame $iframe
$sel update
$sel get {the property you want}
}

you may go to vmd mailing list for more details.

>  Message: 1
>  Date: Tue, 22 Apr 2008 10:42:56 +0800
>  From: Dechang Li <[EMAIL PROTECTED]>
>  Subject: [gmx-users] Re: the number of water molecules (Jian Zou)
>  To: "gmx-users@gromacs.org" 
>  Message-ID: <[EMAIL PROTECTED]>
>  Content-Type: text/plain;   charset="gb2312"
>
>
>  >
>  >Message: 2
>  >Date: Mon, 21 Apr 2008 10:43:27 -0400
>  >From: "Jian Zou" <[EMAIL PROTECTED]>
>  >Subject: [gmx-users] Re: the number of water molecules
>  >To: gmx-users@gromacs.org
>  >Message-ID:
>  >   <[EMAIL PROTECTED]>
>  >Content-Type: text/plain; charset=ISO-8859-1
>  >
>  >How about using vmd selection "within" to do this
>
>   I have tried this. However, vmd can tell me the number in this
>  frame, but there are about 5000 frames! I am tring to write a script
>  to let vmd explore the results to a file VS. frames. If I make
>  any progress, let you know. ^_^
>
>
>  >
>  >>  Message: 3
>  >>  Date: Sun, 20 Apr 2008 21:01:57 +0800
>  >>  From: Dechang Li <[EMAIL PROTECTED]>
>  >>  Subject: [gmx-users] the number of water molecules
>  >>  To: "gmx-users" 
>  >>  Message-ID: <[EMAIL PROTECTED]>
>  >>  Content-Type: text/plain;   charset="gb2312"
>  >>
>  >>  Dear all,
>  >>
>  >> How can I calculate the number of water molecules around the
>  >>  protein with a distance about 5 angstrom? Is that possible in
>  >>  Gromacs?
>  >>
>  >>
>  >>
>  >>  Best regards,
>  >>
>  >>  2008-4-20
>  >>
>  >>
>  >>  =
>  >>  Dechang Li, PhD Candidate
>  >>  Department of Engineering Mechanics
>  >>  Tsinghua University
>  >>  Beijing 100084
>  >>  PR China
>  >>
>  >>  Tel:   +86-10-62773779(O)
>  >>  Email: [EMAIL PROTECTED]
>  >>  =
>  >>
>  >
>  >
>  >--
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Re: [gmx-users] grompp error, invalid line in .gro file

[Andreas Kring]

Justin A. Lemkul skrev:

Just thinking out loud, but maybe "Argon" is too long of a name for the
residues.  The longest I think I've seen is 4 characters (something like LYSH
or ARGN, for example).  Maybe the length of the name is throwing off the
formatting.  Why don't you try again with a residue name of something like AR
(in both the .top and .gro, of course) and see if that fixes things.


It doesn't seem to work... I've tried the topology file below (with a 
similar change in the .gro file)...


Kind regards
Andreas



; Topology file for Ar

; Parameter level

#include "ffoplsaa.itp"
;#define _FF_OPLS
;#define _FF_OPLSAA
;[defaults]
;#include "ffoplsaanb.itp"
;   [atomtypes]
;#include "ffoplsaabon.itp"
;   [bondtypes]
;   [constrainttypes]
;   [angletypes]
;   [dihedraltypes]

; Molecule level

[ moleculetype ]
; molname   nrexcl
Arg 1

[ atoms ]
; idat_type res_nr  res_nameat_name cg_nr   charge
1   opls_0971   Arg Ar  1   0.0

; System level

[ system ]
Argon liquid

[ molecules ]
Arg 2048






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RE: [gmx-users] grompp error, invalid line in .gro file

[Berk Hess]

Hi,

Your formatting is incorrect.
The .gro format is a very old GROMOS fixed format (not free format).
See the manual for the details:
http://www.gromacs.org/documentation/reference/online/gro.html

Berk.

> Date: Tue, 22 Apr 2008 12:12:17 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] grompp error, invalid line in .gro file
> 
> Hello all.
> 
> I'm trying to simulate an argon liquid. The OPLS-AA force field is used 
> with the files from /usr/local/gromacs/share/gromacs/top. But I get an 
> error when I run
> 
> $ grompp -f NVT.mdp -c Ar.gro -p Ar.top
> ---
> Program grompp, VERSION 3.3.3
> Source code file: confio.c, line: 709
> 
> Fatal error:
> Invalid line in Ar.gro for atom 1:
> 1Argon Ar 1 0.0 0.0 0.0
> ---
> 
> An ideas on what can be wrong? My argon .top file and .gro file can be 
> seen below.
> 
> Kind regards
> Andreas
> 
> --
> Ar.top
> --
> ; Topology file for Ar
> 
> ; Parameter level
> 
> #include "ffoplsaa.itp"
> ;#define _FF_OPLS
> ;#define _FF_OPLSAA
> ;[defaults]
> ;#include "ffoplsaanb.itp"
> ;   [atomtypes]
> ;#include "ffoplsaabon.itp"
> ;   [bondtypes]
> ;   [constrainttypes]
> ;   [angletypes]
> ;   [dihedraltypes]
> 
> ; Molecule level
> 
> [ moleculetype ]
> ; molname nrexcl
> Argon 1
> 
> [ atoms ]
> ; id  at_type res_nr  res_nameat_name cg_nr   charge
> 1 opls_0971   Argon   Ar  1   0.0
> 
> ; System level
> 
> [ system ]
> Argon liquid
> 
> [ molecules ]
> Argon 2048
> 
> -
> Ar.gro
> -
> fcc lattice of argon atoms
> 2048
> 1Argon Ar 1 0.0 0.0 0.0
> 2Argon Ar 2 0.283835 0.283835 0.0
> ...
> 2047Argon Ar 2047 4.257525 3.97369 4.257525
> 2048Argon Ar 2048 3.97369 4.257525 4.257525
> 4.54136 4.54136 4.54136
> 
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Re: [gmx-users] grompp error, invalid line in .gro file

[Mark Abraham]

Berk Hess wrote:

Hi,

Your formatting is incorrect.
The .gro format is a very old GROMOS fixed format (not free format).
See the manual for the details:
http://www.gromacs.org/documentation/reference/online/gro.html


Thanks for the link - I remember asking for it on this list years ago :-)

I've now added it to the wiki.

Mark
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[gmx-users] Re: x2top error in CNT simulation (David van der Spoel)

[Hero]

Dear Gromacs,

Actually, the error is for all the 144 atoms on SWNT_6_6_144:

when I ran:
x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

Error message appeared:
Can not find forcefield for atom C-1 with 2 bonds
.
Can not find forcefield for atom C-143 with 2 bonds
Can not find forcefield for atom C-144 with 2 bonds
 ---
Program x2top, VERSION 3.3.3
Source code file: x2top.c, line: 206

Fatal error:
Could only find a forcefield type for 0 out of 144 atoms
---

Could you please tell me what is the problem? Suppose this code should work 
without any problems since it has been on web for a long while.

Or problems showed up after Gromacs 3.3?

Thanks a lot!

Jue

> Dear All,
> 
> I am trying to simulate water flow in CNT and just followed the website:
> http://cs86.com/CNSE/SWNT.htm
> 
> I did the following:
> 
> 1. ffgmx.n2t
>  must change this files name to ffencadv.n2t and add the following 2 
> lines:
> C C 1 C ; CNT Carbon with one bond
> C C 2 C C ; CNT double bonded Carbon
> 
> 2. ffgmxbon.itp
> add the following line to it:
> 
> #
> [ bondtypes ]
> ; i j func b0 kb
> C C 1 0.14210 478900.
> #
> [ angletypes ]
> ; i j k func th0 cth
> C C C 1 120.000 397.480
> #
> [ dihedraltypes ]
> ; i l func q0 cq
> C C 1 0.000 167.360
> #
> 
> But when I ran:
> x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp
> 
> Error message appeared:
> 
> Can not find forcefield for atom C-143 with 2 bonds
> Can not find forcefield for atom C-144 with 2 bonds
> 
> ---
> Program x2top, VERSION 3.3.3
> Source code file: x2top.c, line: 206
> 
> Fatal error:
> Could only find a forcefield type for 0 out of 144 atoms
> ---
> Could you please tell me what is the problem?

x2top -pbc
where are these atoms, on the edge of the CNT? Is your box size correct 
such that you have a periodic CNT?


  

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Re: [gmx-users] Re: x2top error in CNT simulation (David van der Spoel)

[David van der Spoel]

Hero wrote:

Dear Gromacs,

Actually, the error is for all the 144 atoms on SWNT_6_6_144:

when I ran:
x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

Error message appeared:
Can not find forcefield for atom C-1 with 2 bonds
.
Can not find forcefield for atom C-143 with 2 bonds
Can not find forcefield for atom C-144 with 2 bonds
 ---


SHouldn't the carbons have three bonds? Is your input file really ok?



Program x2top, VERSION 3.3.3
Source code file: x2top.c, line: 206

Fatal error:
Could only find a forcefield type for 0 out of 144 atoms
---

Could you please tell me what is the problem? Suppose this code should work 
without any problems since it has been on web for a long while.


Or problems showed up after Gromacs 3.3?

Thanks a lot!

Jue


Dear All,

I am trying to simulate water flow in CNT and just followed the website:
http://cs86.com/CNSE/SWNT.htm

I did the following:

1. ffgmx.n2t
 must change this files name to ffencadv.n2t and add the following 2 lines:
C C 1 C ; CNT Carbon with one bond
C C 2 C C ; CNT double bonded Carbon

2. ffgmxbon.itp
add the following line to it:

#
[ bondtypes ]
; i j func b0 kb
C C 1 0.14210 478900.
#
[ angletypes ]
; i j k func th0 cth
C C C 1 120.000 397.480
#
[ dihedraltypes ]
; i l func q0 cq
C C 1 0.000 167.360
#

But when I ran:
x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

Error message appeared:

Can not find forcefield for atom C-143 with 2 bonds
Can not find forcefield for atom C-144 with 2 bonds

---
Program x2top, VERSION 3.3.3
Source code file: x2top.c, line: 206

Fatal error:
Could only find a forcefield type for 0 out of 144 atoms
---
Could you please tell me what is the problem?


x2top -pbc
where are these atoms, on the edge of the CNT? Is your box size correct 
such that you have a periodic CNT?



  

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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] genbox memory problem

[LuLanyuan]

Hello,
I have a problem about genbox command in GMX. I'm running genbox to randamly 
insert molecules. Because the probobility of successful insertion is low, I 
have to use a large number for the "-try" variable. After running genbox I 
found sometimes the memory cost increased gradually after each unsuccessful 
inserion attempt and finally went beyond the limit of hardware. The memory cost 
went back to a very small number after one successful insertion. I'm wondering 
if it's a memory leakage problem. In my unsterstanding the memory cost 
shouldn't increase after each unsuccessful insertion.  Is that because some 
momeory is not freed after each try?
Thanks.
Lanyuan Lu
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[gmx-users] How to center my trimer in my simulation box.

[Ilya Chorny]

Hello,

I am simulating a trimer in a membrane. In one of my simulation  two of the
monomers are on one side of the box and the other monomer is on the other
side of the box. I tried using trjconv to center the whole thing in the
center of my simulation cell but have failed miserably. I also searched
around for about an hour and could not find anything.

I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.

Any advice?

Thanks,

Ilya

-- 
Ilya Chorny Ph.D.
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Re: [gmx-users] How to center my trimer in my simulation box.

[Xavier Periole]

On Tue, 22 Apr 2008 14:14:19 -0700
 "Ilya Chorny" <[EMAIL PROTECTED]> wrote:

Hello,

I am simulating a trimer in a membrane. In one of my simulation  two of the
monomers are on one side of the box and the other monomer is on the other
side of the box. I tried using trjconv to center the whole thing in the
center of my simulation cell but have failed miserably. I also searched
around for about an hour and could not find anything.

I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.

first run
trjconv -pbc nojump

Any advice?

Thanks,

Ilya

--
Ilya Chorny Ph.D.


-
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-
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Re: [gmx-users] How to center my trimer in my simulation box.

[Ilya Chorny]

Just to clarify.
I would run

trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro?

What would I run next?

Thanks,

Ilya


On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <[EMAIL PROTECTED]> wrote:

> On Tue, 22 Apr 2008 14:14:19 -0700
>  "Ilya Chorny" <[EMAIL PROTECTED]> wrote:
>
> > Hello,
> >
> > I am simulating a trimer in a membrane. In one of my simulation  two of
> > the
> > monomers are on one side of the box and the other monomer is on the
> > other
> > side of the box. I tried using trjconv to center the whole thing in the
> > center of my simulation cell but have failed miserably. I also searched
> > around for about an hour and could not find anything.
> >
> > I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.
> >
> first run
> trjconv -pbc nojump
>
> > Any advice?
> >
> > Thanks,
> >
> > Ilya
> >
> > --
> > Ilya Chorny Ph.D.
> >
>
> -
> XAvier Periole - PhD
>
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -
> ___
> gmx-users mailing listgmx-users@gromacs.org
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-- 
Ilya Chorny Ph.D.
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Re: [gmx-users] How to center my trimer in my simulation box.

[Ilya Chorny]

So I got it to center my protein (using -pbc nojump)  and keep the trimer
and the membrane in tact but it completely destroyed my water. I was hoping
I could get the whole simulation box back with the protein in the center.
Is that possible?

Thanks,

Ilya


On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny <[EMAIL PROTECTED]> wrote:

> Just to clarify.
> I would run
>
> trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro?
>
> What would I run next?
>
> Thanks,
>
> Ilya
>
>
> On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <[EMAIL PROTECTED]> wrote:
>
> > On Tue, 22 Apr 2008 14:14:19 -0700
> >  "Ilya Chorny" <[EMAIL PROTECTED]> wrote:
> >
> > > Hello,
> > >
> > > I am simulating a trimer in a membrane. In one of my simulation  two
> > > of the
> > > monomers are on one side of the box and the other monomer is on the
> > > other
> > > side of the box. I tried using trjconv to center the whole thing in
> > > the
> > > center of my simulation cell but have failed miserably. I also
> > > searched
> > > around for about an hour and could not find anything.
> > >
> > > I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.
> > >
> > first run
> > trjconv -pbc nojump
> >
> > > Any advice?
> > >
> > > Thanks,
> > >
> > > Ilya
> > >
> > > --
> > > Ilya Chorny Ph.D.
> > >
> >
> > -
> > XAvier Periole - PhD
> >
> > NMR & Molecular Dynamics Group
> > University of Groningen
> > The Netherlands
> > http://md.chem.rug.nl/~periole 
> > -
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Ilya Chorny Ph.D.
>



-- 
Ilya Chorny Ph.D.
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Re: [gmx-users] How to center my trimer in my simulation box.

[Alan Dodd]

I've often found it necessary to do multiple trjconv steps to get the result I 
want.  So in this case, I'd probably make sure my protein is genuinely centered 
in the box, then take that output .xtc and then make sure everything is whole 
and approximately in the box (-pbc whole).


- Original Message 
From: Ilya Chorny <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Sent: Tuesday, April 22, 2008 11:52:23 PM
Subject: Re: [gmx-users] How to center my trimer in my simulation box.

So I got it to center my protein (using -pbc nojump)  and keep the trimer and 
the membrane in tact but it completely destroyed my water. I was hoping I could 
get the whole simulation box back with the protein in the center.  Is that 
possible?

Thanks,

Ilya



On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny <[EMAIL PROTECTED]> wrote:

Just to clarify.


I would run


trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro?


What would I run next?


Thanks,


Ilya



On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <[EMAIL PROTECTED]> wrote:

On Tue, 22 Apr 2008 14:14:19 -0700
 "Ilya Chorny" <[EMAIL PROTECTED]> wrote:

Hello,

I am simulating a trimer in a membrane. In one of my simulation  two of the
monomers are on one side of the box and the other monomer is on the other
side of the box. I tried using trjconv to center the whole thing in the
center of my simulation cell but have failed miserably. I also searched
around for about an hour and could not find anything.

I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.

first run
trjconv -pbc nojump


Any advice?

Thanks,

Ilya

-- 
Ilya Chorny Ph.D.



-
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-
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-- 
Ilya Chorny Ph.D.




-- 
Ilya Chorny Ph.D.


  

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Re: [gmx-users] Loop displacement calculation?

[SeungPyo Hong]

Thank you very much Mark~

On Tue, Apr 22, 2008 at 4:27 PM, Mark Abraham <[EMAIL PROTECTED]>
wrote:

> SeungPyo Hong wrote:
>
> > Thank you for your kind response.
> >
> > I think that I do not clearly describe the system.
> >
> > The loop I mentioned above seems to interact with the other parts of the
> > protein with hydrophobic interactions.
> > So, the displacement of the loop from the original position will make
> > the free energy difference, and this can estimate the energy stabilized by
> > the loop placement on its natural form.
> >
> > Is this statement seems to be reasonable?
> >
>
> That makes a lot more sense, however I don't have the expertise to judge
> whether there's a better method around.
>
>  Frankly I am not understanding the free energy calculation method, and
> > maybe it is the reason why I think that this simulation works.
> > I premised that if the free energy code really calculate the free energy
> > a certain ensenble of microstates, it can be used to test the stability of
> > the part of the protein.
> >
>
> Follow the links here
> http://wiki.gromacs.org/index.php/Special:Search?search=free+energy&go=Gofor 
> some tutorial material. Obviously, you will only ever calculate free
> energy *differences*.
>
>
> Mark
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-- 
--
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
[EMAIL PROTECTED]
[EMAIL PROTECTED]
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[gmx-users] how to use GROMACS to model carbon nanotubes

[Christopher Stiles]

I have put together this general response to the vast amounts of e-mails I
have been receiving as of late in regards to how to use GROMACS to model
carbon nanotubes.

 

 New GROMACS Users 

 

First if you are new to GROMACS step on before you even install the program
is to read the manual! It is not that long and it will keep you from making
your self look stupid by asking questions that are very clearly covered in
it.

 

Second run the tutorials and make sure that your installation is functioning
properly.

 

Third make sure that all your files are UNIX formatted while this can cause
major problems otherwise.

 

Fourth become familiar with the formatting of a *.pdb file and what exactly
a residue is!

 

 New to Simulations Containing CNT's 

 

Now once you have done all of this you are ready to start learning how to
use GROMACS for your CNT simulations.

 

First I would start with using my site to get a general idea of what a basic
run through for a CNT simulation entails:

  http://cs86.com/CNSE/SWNT.htm

! Please note that this has not been updated for changes in the most
current version.

 

For *.pdb files you might want to use an application called Nanotube
Modeler, it can be found at  
http://www.jcrystal.com/products/wincnt/

It allows for larger nanotubes then the method I have on the site and even
offers the ability to use capped tubes. I have worked with the developer to
make it so that the output *.pdb files have correct bond records although
note that some modification must be made to the files (commenting out the
first I believe 2 lines or so, and naming your residues properly. This can
be looked up easily and you should know how since you know what a residue is
by now and where they are in your *.pdb file). The application does cost
money but the time you save not hand coding is invaluable.

 

 

 When You Start Having Problems 

 

So when you start having problems which will probably be early and often if
you are anything like me!

 

First consult the Gromacs wiki it can be found at:

http://wiki.gromacs.org/index.php/Main_Page 

 

Next search the mailing list to see if your problem has already been solved,
more then likely it has, and you can do that at the following:

 
http://www.gromacs.org/component/option,com_wrapper/Itemid,165/

 Make sure you check the appropriate boxes for your search, i.e.
'Mailing Lists' This is how I figured out most of my problems and the ones I
asked are also documented, try searching things like 'cnt' and 'swcnt' or
even looking for threads involving me (Christopher Stiles) they would have
been from the summer months of 2007 mainly.

 

 

When all else fails ask your question clearly on the mailing list which can
be found:

 

http://www.gromacs.org/index.php?option=com_content&task=view&id=73&Itemid=7
6 

! Please make sure you are very clear while it will save you and the
people nice enough to respond lots of time! So what I mean by being clear is
include any errors you are having as they appeared when you get them. Also
include all step you have made previously including the commands you used
and how you modified any files. 

 

Also VERY IMPORTANT, pose your questions on the mailing list and not
personally to individuals e-mail addresses. This way when this person is
nice enough to take time out of their day to answer your question, others
may benefit from the question and answer.

 

 Analyzing Your Data 

 

Since you have read the manual you know there are lots of great tools built
in! So use them! Although I did run into some problems getting them to do
exactly what I wanted to do so I utilized another application. For my
analysis of my data I use an application called VMD it can be found at the
following address:

http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

With this application I use Tcl/Tk scripts to analyze at the data. This
application is very useful in producing nice images for presentations as
well!

 



 

At any rate that's the best I can do since I am graduating in May. Also
please note that this is just what I learned to do over the last year so I
am no expert by any means, and I am just trying to help others that wish to
attempt similar things. I thank all those that have helped me along the way!

 

Additionally if some one would like to put this on GROMACS's wiki please
feel free to do so, I would but with graduation coming up I don't even have
time to

Re: [gmx-users] How to center my trimer in my simulation box.

[Ilya Chorny]

So I got it to work for my trimer by doing the following.
1.) trjconv -f *.xtc -s *.tpr -pbc nojump -o out.xtc
2.) trjconv -f out.xtc -s *.tpr -pbc mol -center -boxcenter rect

The first step unwraps the whole trajectory and the second step wraps it
back up.

Cheers,

Ilya


-- 
Ilya Chorny Ph.D.

On Tue, Apr 22, 2008 at 4:30 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:

> I've often found it necessary to do multiple trjconv steps to get the
> result I want.  So in this case, I'd probably make sure my protein is
> genuinely centered in the box, then take that output .xtc and then make sure
> everything is whole and approximately in the box (-pbc whole).
>
>
>  - Original Message 
> From: Ilya Chorny <[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users 
> Sent: Tuesday, April 22, 2008 11:52:23 PM
> Subject: Re: [gmx-users] How to center my trimer in my simulation box.
>
> So I got it to center my protein (using -pbc nojump)  and keep the trimer
> and the membrane in tact but it completely destroyed my water. I was hoping
> I could get the whole simulation box back with the protein in the center.
> Is that possible?
>
> Thanks,
>
> Ilya
>
>
> On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny <[EMAIL PROTECTED]> wrote:
>
> > Just to clarify.
> > I would run
> >
> > trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro?
> >
> > What would I run next?
> >
> > Thanks,
> >
> > Ilya
> >
> >
> > On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <[EMAIL PROTECTED]>
> > wrote:
> >
> > > On Tue, 22 Apr 2008 14:14:19 -0700
> > >  "Ilya Chorny" <[EMAIL PROTECTED]> wrote:
> > >
> > > > Hello,
> > > >
> > > > I am simulating a trimer in a membrane. In one of my simulation  two
> > > > of the
> > > > monomers are on one side of the box and the other monomer is on the
> > > > other
> > > > side of the box. I tried using trjconv to center the whole thing in
> > > > the
> > > > center of my simulation cell but have failed miserably. I also
> > > > searched
> > > > around for about an hour and could not find anything.
> > > >
> > > > I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.
> > > >
> > > first run
> > > trjconv -pbc nojump
> > >
> > > > Any advice?
> > > >
> > > > Thanks,
> > > >
> > > > Ilya
> > > >
> > > > --
> > > > Ilya Chorny Ph.D.
> > > >
> > >
> > > -
> > > XAvier Periole - PhD
> > >
> > > NMR & Molecular Dynamics Group
> > > University of Groningen
> > > The Netherlands
> > > http://md.chem.rug.nl/~periole
> > > -
> > > ___
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> > > posting!
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> > > interface or send it to [EMAIL PROTECTED]
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> > >
> >
> >
> >
> > --
> > Ilya Chorny Ph.D.
> >
>
>
>
> --
> Ilya Chorny Ph.D.
>
>
> --
> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it
> now.
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-- 
Ilya Chorny Ph.D.
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Re: [gmx-users] how to use GROMACS to model carbon nanotubes

[Mark Abraham]

> Additionally if some one would like to put this on GROMACS's wiki please
> feel free to do so, I would but with graduation coming up I don't even
> have
> time to be writing this. If you would like the files I have on my site
> those
> can be provided for this purpose as well!

Wikified here http://wiki.gromacs.org/index.php/Carbon_Nanotube.

Thanks, Christopher.

Mark

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Re: [gmx-users] trjconv error

[Ragothaman Yennamalli]

Hi,
Sorry for not replying immediately.

Gromacs ver 3.2.1
OS is Red hat enterprise 4
Initially I had tried reading the file from an external hard disk and now I 
copied it to another system and tried again. Still the same error.
The reason why I was truncating was due to a magic number error I got while 
reading the trajectory.
"Fatal error: Magic Number Error in XTC file (read 0, should be 1995)"
So, I was truncating it at an earlier time from where I didnt see any errors.

Regards,
Raghu 
 


--- On Fri, 18/4/08, Mark Abraham <[EMAIL PROTECTED]> wrote:

> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] trjconv error
> To: "Discussion list for GROMACS users" 
> Date: Friday, 18 April, 2008, 8:09 PM
> Ragothaman Yennamalli wrote:
> > I wanted to truncate a trajectory file and when I use
> > trjconv tool, I get an error:
> > Fatal error:
> > /media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc
> > is not a trj file, exiting
> > 
> > The file is able to read by gmxcheck...
> > 
> > What could be the problem?
> 
> What GROMACS version? What OS? Have you tried copying the
> file elsewhere 
> and reading from there?
> 
> Mark
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Re: [gmx-users] trjconv error

[Mark Abraham]

Ragothaman Yennamalli wrote:

Hi,
Sorry for not replying immediately.

Gromacs ver 3.2.1
OS is Red hat enterprise 4
Initially I had tried reading the file from an external hard disk and now I 
copied it to another system and tried again. Still the same error.
The reason why I was truncating was due to a magic number error I got while 
reading the trajectory.
"Fatal error: Magic Number Error in XTC file (read 0, should be 1995)"
So, I was truncating it at an earlier time from where I didnt see any errors.


Dunno. 3.2.1 is a very old version - you should be planning your upgrade 
to version 4 as soon as it's out, unless you need compatibility for some 
reason.


Otherwise the only reason I can think that gmxdump might succeed where 
trjconv doesn't is that it isn't actually an XTC file, but some other 
format with an .xtc extension.


Try to replicate your problem with a small simulation. If you can, then 
you probably have a real issue, but this is very unlikely. If you can't 
replicate it, then it seems you've probably mangled something and we 
can't help you.


Mark
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