date:20110111

Re: [gmx-users] file heme.rtp

2011-01-11 Thread Justin A. Lemkul




Tanos Franca wrote:

Dear Gromacs users,
I'm sure that the Gromos5A36 force field have topology to the heme 
group and would like to know how to proceed to perform a successfull MD 
simulation on a protein with this group. Should I just write the name of 
the heme topology file inside the protein.top file (just like we do with 
ions.itp) ? We also would like to confirm the name of the heme topology 
file. Is it heme.rtp ?


No.  The heme group is defined in aminoacids.rtp as HEME, and any special bonds 
between the heme prosthetic group and amino acid sidechains is handled by 
specbond.dat, thus the heme becomes part of the protein moleculetype.


That said, there have been plenty of posts to the list that there are errors 
when running grompp (missing bond and angle parameters, usually) such that the 
presence of heme groups may not work out of the box, so to speak.  Of course, 
plenty of heme simulations have been reported in the literature, so those bonded 
parameters must exist somewhere.


-Justin


Thank you in advance.
Tanos C. C. Franca.
Coordinator of the Graduate Program in Chsmistry.
Military Intitute of Engineering.
Rio de Janeiro - RJ
Brazil.


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] file heme.rtp

2011-01-11 Thread Tanos Franca


Dear Gromacs users,
I'm sure that the Gromos5A36 force field have topology to the heme 
group and would like to know how to proceed to perform a successfull MD 
simulation on a protein with this group. Should I just write the name of 
the heme topology file inside the protein.top file (just like we do with 
ions.itp) ? We also would like to confirm the name of the heme topology 
file. Is it heme.rtp ?

Thank you in advance.
Tanos C. C. Franca.
Coordinator of the Graduate Program in Chsmistry.
Military Intitute of Engineering.
Rio de Janeiro - RJ
Brazil.
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Re: [gmx-users] g_density CHARMM

2011-01-11 Thread Ramon Guixà

Thanks again Justin

-Original Message-
From: Justin A. Lemkul 
Reply-to: "jalem...@vt.edu" , Discussion list for
GROMACS users 
To: Gromacs Users' List 
Subject: Re: [gmx-users] g_density CHARMM
Date: Tue, 11 Jan 2011 22:08:22 +0100



Ramon Guixà wrote:
> Justin,
> Thanks for your response.
> The membranes I've already run are made of POPC and cholesterol, so the 
> sphingomyelin membrane is my next simulation but I haven't managed to 
> find a proper forcefield for it. Would you know where to find this?

Not for CHARMM, no, but there are several available for different Gromos force 
fields.

http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml (contact Prof. Karttunen for 
the topology)

-Justin

> Ramon
> 
> -Original Message-
> *From*: Justin A. Lemkul  >
> *Reply-to*: "jalem...@vt.edu" , Discussion list for 
> GROMACS users 
> *To*: Discussion list for GROMACS users  >
> *Subject*: Re: [gmx-users] g_density CHARMM
> *Date*: Tue, 11 Jan 2011 19:45:58 +0100
> 
> 
> Ramon Guixà wrote:
>> 
>> Dear all,
>> 
>> I am just a newbie to Gromacs so sorry for being naive with my questions...
>> 
>> I would like to yield electron density profiles out of different 
>> trajectories of membranes simulated with NAMD and last CHARMM forcefield 
>> (all_36_lipid_cholesterol). I first tried to use pdb2gmx in order to 
>> generate a GROMACS topology file that I could use for generating the 
>> .tpr file needed for g_density. Well, I did not manage but is this the 
>> proper way though?
> 
> Not likely.  pdb2gmx is useful for creating topologies of macromolecules 
> built 
> of repeating units (i.e. proteins and polymers).  For lipid bilayers, it is 
> far 
> more common to construct the topology as a set of #include statements, i.e.:
> 
> #include (forcefield)
> 
> #include "first_lipid_type.itp"
> #include "next_lipid_type.itp"
> 
> etc.
> 
>> Also, so far all my trajectories are .dcd files; does the g_density 
>> function needs a .pdb file per frame? Otherwise, is it possible to 
>> directly convert .dcd files into the gromacs .xtc ones?
>> 
> 
> Newer versions of Gromacs (>4.5) can read any file format that VMD can read, 
> so 
> conversion is not necessary, provided you have the VMD libraries installed.
> 
>> On another note, would anyone know where could I get proper topology and 
>> parameter files of sphingomyelin?
>> 
> 
> If you already ran the simulations, do you not already have this?  With the 
> information in Chapter 5 of the manual, you should be able to convert your 
> topologies from whatever format you have it in into the one required by 
> Gromacs.
> 
> -Justin
> 
>> Many thanks in advance!
>> 
>> Ramon
>> 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 

-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Simulations in vacuo

2011-01-11 Thread Mark Abraham


On 12/01/2011 2:29 AM, Zoe Hall wrote:


Hi gmx-users,

I am trying to set up a simulation of a large protein /in vacuo/ using 
the OPLS-AA forcefield, with conditions based on Patriksson et. al 
(Biochemistry 2007, 46 p933).  Basically after energy minimisation, 
the protein is run for 10ps in vacuum with constant temperature at 
300K. This is followed by the full production run of 10ns with 
temperature and pressure coupling turned off, H bonds are constrained 
using SHAKE with tolerance 0.001. For vacuum conditions, the periodic 
boundary conditions are turned off, and no cut-offs are used whatsoever.


I am not sure, however, what is the appropriate choice for 
"coulombtype" and other electrostatic parameters for vacuum 
simulations. I have set "epsilon_r" to 2, as this seems to be an 
accepted value for proteins but if anyone has comments on this, I 
would appreciate it.




vdwtype = cut-off
coulombtype = cut-off

and all the distance cut-offs to zero (which is treated as an infinite 
cut-off)


Mark
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RE: [gmx-users] perfluorohexane pdb... again

2011-01-11 Thread Ángel Piñeiro

Hi Marcelo
your initial box is right, (4.72 nm)^3 = 105.15404e-27 m^3
500 hexane molecules = 500/(6.02e23)*86.16e-3 kg
the density of your initial system = 680.200377454 kg m^-3

The pdb file you sent contained two different structures (I just
realized about this) the first one is in a box of the right dimensions
but the second one, I guess the final frame, is in a much larger box
(8.1315 nm each edge). Your SA at 1000 K and at constant pressure
expands the system a lot and you are not simulating long enough at 298 K
to go back to the right density, that's all.

Cheers,

Ángel.

On Tue, 2011-01-11 at 21:27 +, Marcelo Silva wrote:

> Hi Angél,
> 
> Packmol doesn't add the box dimensions in the pdb, but I've created a
> cube with side 4.72 nm in the input file.

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Re: [gmx-users] RB Dihedrals with ffamber96 in Gromacs 4.5.3?

2011-01-11 Thread Mark Abraham


On 12/01/2011 2:50 AM, RJ Nowling wrote:

Hi all,

This is my first time posting to the list, so please excuse any
ignorance on my part.  I'm preparing a few test systems using Gromacs
4.5.3 with the ffamber96 forcefield.  When I use gmxdump on the
resulting tprs, I see Proper Dihedrals but not RB Dihedrals.  Does
ffamber96 use RB Dihedrals and is it an expected result to not contain
RB Dihedrals?  For reference, I'm preparing DHFR and a ww mutant.


Check out the contents of the [dihedraltypes] section of 
$GMXLIB/share/top/amber96.ff/ffbonded.itp in context of manual Table 
5.5. When preparing topologies for new systems, knowledge of chapter 5 
of the manual will never go astray.


Mark
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Re: [gmx-users] Tautomer Prediction

2011-01-11 Thread Mark Abraham


On 12/01/2011 8:11 AM, Nancy wrote:

Hi All,

Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value 
of the acidic hydrogen on the thiazolidinedione ring of pioglitazone 
is 4.57 (see attached "Figure_1.gif").  Therefore, the predominant 
species at pH 7.0 predicted by MarvinSketch is the one depicted in 
"Figure_2.gif".  The different tautomeric forms predicted by 
MarvinSketch are shown in "Figure_3.gif".


Can anyone explain where these predictions come from, and if they are 
correct?


Nancy, this is a forum for discussion of questions relating to the 
biomolecular simulation package GROMACS. Your questions would be more 
suited to a general chemistry discussion forum, though I can't suggest a 
particular one. At the very least, you would have to read the 
documentation of the software you've used, and any underlying scientific 
literature to start answering your own questions.


Mark
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Re: [gmx-users] perfluorohexane pdb... again

2011-01-11 Thread Ángel Piñeiro

Hi Marcelo
your molecules are not in a box, the head of the pdb you sent to me is:

HEADER 
TITLE Built with
Packmol 
REMARK   Packmol generated pdb file 
REMARK   Home-Page: http://www.ime.unicamp.br/~martinez/packmol
REMARK
ATOM  1  C1  HEX A   1  17.953  31.169   8.840  1.00 20.00
C+0
ATOM  2  C2  HEX A   1  18.510  32.451   9.461  1.00 20.00
C+0
ATOM  3  C3  HEX A   1  18.321  33.614   8.486  1.00 20.00
C+0
ATOM  4  C4  HEX A   1  18.878  34.896   9.108  1.00 20.00
C+0
ATOM  5  C5  HEX A   1  18.689  36.059   8.133  1.00 20.00
C+0


there are no walls there.

Cheers,

Ángel.



On Tue, 2011-01-11 at 20:31 +, Marcelo Silva wrote:

> Angél,
> 
> I'm sending you my initial pdb in attachment. I chose the box size to 
> fit the experimental density.
> I am just trying to get simple properties of the pure compounds hexane 
> and perfluorohexane and of a mixture 0.5 hexane/perfluorohexane (density 
> mainly). But maybe I just need a long molecular dynamics equilibation 
> step rather than simulated annealing to get a good starting configuration.
> Perhaps what went "wrong" is that the system was at temperatures much 
> higher than hexane boiling point and it started to form clusters.
> 
> Best regards,
> 
> Marcelo


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[gmx-users] Tautomer Prediction

2011-01-11 Thread Nancy

Hi All,

Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value of
the acidic hydrogen on the thiazolidinedione ring of pioglitazone is 4.57
(see attached "Figure_1.gif").  Therefore, the predominant species at pH 7.0
predicted by MarvinSketch is the one depicted in "Figure_2.gif".  The
different tautomeric forms predicted by MarvinSketch are shown in
"Figure_3.gif".

Can anyone explain where these predictions come from, and if they are
correct?

Thanks,
Nancy
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Re: [gmx-users] g_density CHARMM

2011-01-11 Thread Justin A. Lemkul




Ramon Guixà wrote:

Justin,
Thanks for your response.
The membranes I've already run are made of POPC and cholesterol, so the 
sphingomyelin membrane is my next simulation but I haven't managed to 
find a proper forcefield for it. Would you know where to find this?


Not for CHARMM, no, but there are several available for different Gromos force 
fields.


http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml (contact Prof. Karttunen for 
the topology)


-Justin


Ramon

-Original Message-
*From*: Justin A. Lemkul >
*Reply-to*: "jalem...@vt.edu" , Discussion list for 
GROMACS users 
*To*: Discussion list for GROMACS users >

*Subject*: Re: [gmx-users] g_density CHARMM
*Date*: Tue, 11 Jan 2011 19:45:58 +0100


Ramon Guixà wrote:


Dear all,

I am just a newbie to Gromacs so sorry for being naive with my questions...

I would like to yield electron density profiles out of different 
trajectories of membranes simulated with NAMD and last CHARMM forcefield 
(all_36_lipid_cholesterol). I first tried to use pdb2gmx in order to 
generate a GROMACS topology file that I could use for generating the 
.tpr file needed for g_density. Well, I did not manage but is this the 
proper way though?


Not likely.  pdb2gmx is useful for creating topologies of macromolecules built 
of repeating units (i.e. proteins and polymers).  For lipid bilayers, it is far 
more common to construct the topology as a set of #include statements, i.e.:


#include (forcefield)

#include "first_lipid_type.itp"
#include "next_lipid_type.itp"

etc.

Also, so far all my trajectories are .dcd files; does the g_density 
function needs a .pdb file per frame? Otherwise, is it possible to 
directly convert .dcd files into the gromacs .xtc ones?




Newer versions of Gromacs (>4.5) can read any file format that VMD can read, so 
conversion is not necessary, provided you have the VMD libraries installed.


On another note, would anyone know where could I get proper topology and 
parameter files of sphingomyelin?




If you already ran the simulations, do you not already have this?  With the 
information in Chapter 5 of the manual, you should be able to convert your 
topologies from whatever format you have it in into the one required by Gromacs.


-Justin


Many thanks in advance!

Ramon



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] perfluorohexane pdb... again

2011-01-11 Thread Marcelo Silva


Angél,

I'm sending you my initial pdb in attachment. I chose the box size to 
fit the experimental density.
I am just trying to get simple properties of the pure compounds hexane 
and perfluorohexane and of a mixture 0.5 hexane/perfluorohexane (density 
mainly). But maybe I just need a long molecular dynamics equilibation 
step rather than simulated annealing to get a good starting configuration.
Perhaps what went "wrong" is that the system was at temperatures much 
higher than hexane boiling point and it started to form clusters.


Best regards,

Marcelo
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Re: [gmx-users] g_density CHARMM

2011-01-11 Thread Ramon Guixà

Justin, 
Thanks for your response.
The membranes I've already run are made of POPC and cholesterol, so the
sphingomyelin membrane is my next simulation but I haven't managed to
find a proper forcefield for it. Would you know where to find this?
Ramon

-Original Message-
From: Justin A. Lemkul 
Reply-to: "jalem...@vt.edu" , Discussion list for
GROMACS users 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] g_density CHARMM
Date: Tue, 11 Jan 2011 19:45:58 +0100

Ramon Guixà wrote:
> 
> Dear all,
> 
> I am just a newbie to Gromacs so sorry for being naive with my questions...
> 
> I would like to yield electron density profiles out of different 
> trajectories of membranes simulated with NAMD and last CHARMM forcefield 
> (all_36_lipid_cholesterol). I first tried to use pdb2gmx in order to 
> generate a GROMACS topology file that I could use for generating the 
> .tpr file needed for g_density. Well, I did not manage but is this the 
> proper way though?

Not likely.  pdb2gmx is useful for creating topologies of macromolecules built 
of repeating units (i.e. proteins and polymers).  For lipid bilayers, it is far 
more common to construct the topology as a set of #include statements, i.e.:

#include (forcefield)

#include "first_lipid_type.itp"
#include "next_lipid_type.itp"

etc.

> Also, so far all my trajectories are .dcd files; does the g_density 
> function needs a .pdb file per frame? Otherwise, is it possible to 
> directly convert .dcd files into the gromacs .xtc ones?
> 

Newer versions of Gromacs (>4.5) can read any file format that VMD can read, so 
conversion is not necessary, provided you have the VMD libraries installed.

> On another note, would anyone know where could I get proper topology and 
> parameter files of sphingomyelin?
> 

If you already ran the simulations, do you not already have this?  With the 
information in Chapter 5 of the manual, you should be able to convert your 
topologies from whatever format you have it in into the one required by Gromacs.

-Justin

> Many thanks in advance!
> 
> Ramon
> 

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] g_density CHARMM

2011-01-11 Thread Justin A. Lemkul




Ramon Guixà wrote:


Dear all,

I am just a newbie to Gromacs so sorry for being naive with my questions...

I would like to yield electron density profiles out of different 
trajectories of membranes simulated with NAMD and last CHARMM forcefield 
(all_36_lipid_cholesterol). I first tried to use pdb2gmx in order to 
generate a GROMACS topology file that I could use for generating the 
.tpr file needed for g_density. Well, I did not manage but is this the 
proper way though?


Not likely.  pdb2gmx is useful for creating topologies of macromolecules built 
of repeating units (i.e. proteins and polymers).  For lipid bilayers, it is far 
more common to construct the topology as a set of #include statements, i.e.:


#include (forcefield)

#include "first_lipid_type.itp"
#include "next_lipid_type.itp"

etc.

Also, so far all my trajectories are .dcd files; does the g_density 
function needs a .pdb file per frame? Otherwise, is it possible to 
directly convert .dcd files into the gromacs .xtc ones?




Newer versions of Gromacs (>4.5) can read any file format that VMD can read, so 
conversion is not necessary, provided you have the VMD libraries installed.


On another note, would anyone know where could I get proper topology and 
parameter files of sphingomyelin?




If you already ran the simulations, do you not already have this?  With the 
information in Chapter 5 of the manual, you should be able to convert your 
topologies from whatever format you have it in into the one required by Gromacs.


-Justin


Many thanks in advance!

Ramon



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] van der Walls radius and implicit solvation

2011-01-11 Thread Per Larsson

Hi!

Currently there is no support in Gromacs for implicit solvation using a 
united-atom force field.
It is definitely possible though, but you need to consult the literature for 
values for the radii. 
For united-atoms, I guess the hydrogens you mention are the polar hydrogens?

All radii in the current implementation are taken from the literature, in many 
cases though using Tinker as the primary source.

Cheers
/Per

11 jan 2011 kl. 19.19 skrev Diogo Vila Viçosa:

> Hi,
> 
> I have two questions regarding the generalized born models implemented in 
> GROMACS.
> 
> 1) Is it possible to perform an MD run using implicit solvent with an 
> united-atom force field? If so, how are determined the van der Walls radii 
> for H atoms?
> 
> 2) How are determined the other van der walls radii used in GROMACS?
> 
> 
> Thanks in advance
> 
> Diogo Vila Viçosa
> 
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[gmx-users] g_density CHARMM

2011-01-11 Thread Ramon Guixà


Dear all,

I am just a newbie to Gromacs so sorry for being naive with my
questions...

I would like to yield electron density profiles out of different
trajectories of membranes simulated with NAMD and last CHARMM forcefield
(all_36_lipid_cholesterol). I first tried to use pdb2gmx in order to
generate a GROMACS topology file that I could use for generating
the .tpr file needed for g_density. Well, I did not manage but is this
the proper way though?
Also, so far all my trajectories are .dcd files; does the g_density
function needs a .pdb file per frame? Otherwise, is it possible to
directly convert .dcd files into the gromacs .xtc ones?

On another note, would anyone know where could I get proper topology and
parameter files of sphingomyelin?

Many thanks in advance!

Ramon

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RE: [gmx-users] perfluorohexane pdb... again

2011-01-11 Thread Ángel Piñeiro

Hi Marcelo
It is always good to see what happens to a known molecule before working
with your target with a new methodology. I took a closer look to your
pdb. You do have different hexane conformations. Anyway it is hard to
believe that your initial box was full of hexane... could you check
again your initial pdb file? could you paste the head of the initial pdb
file to see the box dimensions? The final pdb file is a cubic box of
4.72 nm each edge. I do knot know what are you looking for with your
system but why don't you run a longer MD simulation at 298 K at constant
pressure to get the right density of the system? you should get a
variety of different reliable conformations with different probability
that you could group in clusters if you are interested in that.

Cheers, 

Ángel.

On Tue, 2011-01-11 at 17:44 +, Marcelo Silva wrote:

> Hello Angél,
> 
> I started with hexane just to know what would happen and then I would
> apply the same procedure to perfluorohexane.
> I used a NPT box with 500 hexane molecules using packmol. The system
> was initially homogeneous.
> 
> Then I ran energy minimization with steepest descent (em.mdp) and the
> simmulated annealing afterwards with no constraints (sa.mdp). It's the
> first time I am using SA as I think this would be a good way of having
> a good starting box. I used the OPLS-AA force field.
> 
> The mdp's are in the attachment. 
> 
> __
> 
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Re: [gmx-users] temperature of different atom groups in the system

2011-01-11 Thread Justin A. Lemkul




Vitaly Chaban wrote:

Hi all,

Is there a trick to analyze the temperatures of the atom groups if
they are not coupled separately? E.g. when the whole system is
T-coupled as the only group, can one determine the temperature
evolution for its parts?



You can use g_traj -ot, but as the help information warns, if constraints are 
applied, you must manually correct for this effect.


-Justin


Thank You.

=
Dr. Vitaly V. Chaban, Ph.D.
Department of Chemistry
University of Rochester
Rochester, New York 14627-0216
The United States of America
=


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ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] van der Walls radius and implicit solvation

2011-01-11 Thread Diogo Vila Viçosa

Hi,

I have two questions regarding the generalized born models implemented in
GROMACS.

1) Is it possible to perform an MD run using implicit solvent with an
united-atom force field? If so, how are determined the van der Walls radii
for H atoms?

2) How are determined the other van der walls radii used in GROMACS?


Thanks in advance

Diogo Vila Viçosa
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RE: [gmx-users] perfluorohexane pdb... again

2011-01-11 Thread Marcelo Silva

I'm sorry to send another message but the sa.mdp file I sent was an old one

Best regards

From: jokle...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] perfluorohexane pdb... again
Date: Tue, 11 Jan 2011 17:44:50 +

Hello Angél,

I started with hexane just to know what would happen and then I would apply the 
same procedure to perfluorohexane.
I used a NPT box with 500 hexane molecules using packmol. The system was 
initially homogeneous.

Then I ran energy minimization with steepest descent (em.mdp) and the 
simmulated annealing afterwards with no constraints (sa.mdp). It's the first 
time I am using SA as I think this would be a good way of having a good 
starting box. I used the OPLS-AA force field.

The mdp's are in the attachment. 

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sa.mdp
Description: application/mdp
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Re: [gmx-users] perfluorohexane pdb... again

2011-01-11 Thread Ángel Piñeiro

Hi Marcelo
1.- perfluorohexane is a quite rigid molecule so I wouldn't expect many
different conformations
2.- your simulation box is far away from the equilibrium
3.- you should inform about which force field and simulation conditions
are you using, for instance: was your simulation run at constant volume
or constant pressure? it is better if you provide your mdp file and
specify your force field.

Since more than half of your simulation box is empty and the PFH
molecules are aggregates like in cubes it seems clear that you are ages
away from the equilibrium.

Cheers,

Ángel.

On Tue, 2011-01-11 at 16:50 +, Marcelo Silva wrote:

> Thank you Angél and Stephane for your help
> 
> I also have another question. Using the pure hexane pdb (I am mixing 
> hexane and perfluorohexane), I've run simmulated annealing with a box of 
> 500 molecules trying to obtain a good conformer distribution. The 
> heating steps were:
> 
> time (ps): 0  8 50 58 150
> Temperature: 298 1000 298 1000 298
> 
> I don't if this is the best temperature program but I've converted the 
> trajectory to a pdb file (last time step) and using Avogadro I see a box 
> full of hexane molecules but the same conformer. Using Rasmol I see 
> different conformers and the box as several holes in it. What is wrong 
> here?
> 
> pdb link: http://www.filefactory.com/file/b4h4847/n/hexane.pdb
> 
> Thank you again and best regards
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Re: [gmx-users] perfluorohexane pdb... again

2011-01-11 Thread Marcelo Silva


Thank you Angél and Stephane for your help

I also have another question. Using the pure hexane pdb (I am mixing 
hexane and perfluorohexane), I've run simmulated annealing with a box of 
500 molecules trying to obtain a good conformer distribution. The 
heating steps were:


time (ps): 0  8 50 58 150
Temperature: 298 1000 298 1000 298

I don't if this is the best temperature program but I've converted the 
trajectory to a pdb file (last time step) and using Avogadro I see a box 
full of hexane molecules but the same conformer. Using Rasmol I see 
different conformers and the box as several holes in it. What is wrong 
here?


pdb link: http://www.filefactory.com/file/b4h4847/n/hexane.pdb

Thank you again and best regards
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[gmx-users] Geometry-dependent (non-spherically symmetric) potentials

2011-01-11 Thread ms


Hi,

While I understand that all non-bonded gmx potential shapes are intended 
to be spherically symmetric, for a project of mine it would be helpful 
to be able to have a non-bonded pair potential which is 
geometry-dependent (that is, depending on the angle between 3 atoms).


Has anything -official or unofficial- of this kind ever been attempted 
on Gromacs and, if yes, are there code examples to look at?


Any kind of advice is welcome!

thanks,
Massimo

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[gmx-users] temperature of different atom groups in the system

2011-01-11 Thread Vitaly Chaban

Hi all,

Is there a trick to analyze the temperatures of the atom groups if
they are not coupled separately? E.g. when the whole system is
T-coupled as the only group, can one determine the temperature
evolution for its parts?

Thank You.

=
Dr. Vitaly V. Chaban, Ph.D.
Department of Chemistry
University of Rochester
Rochester, New York 14627-0216
The United States of America
=
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[gmx-users] Simulations in vacuo

2011-01-11 Thread Zoe Hall


Hi gmx-users,

I am trying to set up a simulation of a large protein in vacuo using the 
OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 
2007, 46 p933).  Basically after energy minimisation, the protein is run for 
10ps in vacuum with constant temperature at 300K. This is followed by the full 
production run of 10ns with temperature and pressure coupling turned off, H 
bonds are constrained using SHAKE with tolerance 0.001. For vacuum conditions, 
the periodic boundary conditions are turned off, and no cut-offs are used 
whatsoever.

I am not sure, however, what is the appropriate choice for "coulombtype" and 
other electrostatic parameters for vacuum simulations. I have set "epsilon_r" 
to 2, as this seems to be an accepted value for proteins but if anyone has 
comments on this, I would appreciate it.

Thanks very much,

Zoe

Zoe Hall
Department of Chemistry
Oxford University

zoe.h...@chem.ox.ac.uk


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[gmx-users] RB Dihedrals with ffamber96 in Gromacs 4.5.3?

2011-01-11 Thread RJ Nowling

Hi all,

This is my first time posting to the list, so please excuse any
ignorance on my part.  I'm preparing a few test systems using Gromacs
4.5.3 with the ffamber96 forcefield.  When I use gmxdump on the
resulting tprs, I see Proper Dihedrals but not RB Dihedrals.  Does
ffamber96 use RB Dihedrals and is it an expected result to not contain
RB Dihedrals?  For reference, I'm preparing DHFR and a ww mutant.

Thanks,
RJ
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Re: [gmx-users] problem running the demo

2011-01-11 Thread Justin A. Lemkul




Mao Mao wrote:

Hi All,
I ran into a problem when running the methanol example in "Getting 
Started". When I ran "grompp -v", I got the following:
  
  Fatal error:

  Atomtype CMET not found

I installed Gromacs 4.5.3 on Ubuntu and planned to learn the software. 
Now I am stuck. 
Many thanks for your help! I really appreciate it.




There is a typo in the methanol.itp file in the /tutor/methanol subdirectory. 
Replace it with the one from the gromos43a1.ff directory.  There may be more 
errors along the way; I don't think the demo has been updated in some time.


-Justin


Mao


On Wed, Jan 5, 2011 at 4:41 PM, Justin A. Lemkul > wrote:




Mao Mao wrote:

Hi All,
I am a new user of Gromacs and Linux. I am using Ubuntu 10.10
and installed Gromacs 4.5.3 following the instructions. When I
ran the demo, I found that when I pressed , the xterm
window which is supposed to appear separately just flashed and
disappeared immediately. For instance, "the output of the genbox
program should appear in a separate xterm window", but when I
pressed  the window flashed and disappeared immediately.
Is there anything wrong that I need to fix or is that the way it
should be?


It is possible that something is wrong with the demo, but more
likely something is wrong with your X window settings.  If you're
looking for tutorial material, there are far better resources than
this simple walkthrough:

http://www.gromacs.org/Documentation/Tutorials

-Justin

Best,
Mao


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] problem running the demo

2011-01-11 Thread Mao Mao

Hi All,
I ran into a problem when running the methanol example in "Getting Started".
When I ran "grompp -v", I got the following:

  Fatal error:
  Atomtype CMET not found

I installed Gromacs 4.5.3 on Ubuntu and planned to learn the software. Now I
am stuck.
Many thanks for your help! I really appreciate it.

Mao


On Wed, Jan 5, 2011 at 4:41 PM, Justin A. Lemkul  wrote:

>
>
> Mao Mao wrote:
>
>> Hi All,
>> I am a new user of Gromacs and Linux. I am using Ubuntu 10.10 and
>> installed Gromacs 4.5.3 following the instructions. When I ran the demo, I
>> found that when I pressed , the xterm window which is supposed to
>> appear separately just flashed and disappeared immediately. For instance,
>> "the output of the genbox program should appear in a separate xterm window",
>> but when I pressed  the window flashed and disappeared immediately.
>> Is there anything wrong that I need to fix or is that the way it should be?
>>
>
> It is possible that something is wrong with the demo, but more likely
> something is wrong with your X window settings.  If you're looking for
> tutorial material, there are far better resources than this simple
> walkthrough:
>
> http://www.gromacs.org/Documentation/Tutorials
>
> -Justin
>
>  Best,
>> Mao
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Ubuntu Installation

2011-01-11 Thread Sergio Manzetti

Thanks, doing # sudo apt-get install libfftw3-dev fixed the problem

Sergio

On Tue, Jan 11, 2011 at 7:31 AM, Jussi Lehtola wrote:

> On Tue, 11 Jan 2011 07:00:46 -0600
> Sergio Manzetti  wrote:
>
> > Dear users, I have installed FFTW3 successfully, and confirmed its
> > location using locate:
> >
> >
> > However, when I try installing Gromacs 4.5.3 the -/configure step
> > yields:
> >
> > configure: error: Cannot find fftw3f library
> >
> >
> > What am I doing incorrectly?
>
> Looks like you're missing the development package. Run
>
> # apt-get install libfftw3-dev
>
> to fix this.
> --
> --
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.leht...@helsinki.fi
> --
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.leht...@helsinki.fi, p. 191 50632
> --
> --
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Re: [gmx-users] Ubuntu Installation

2011-01-11 Thread Jussi Lehtola

On Tue, 11 Jan 2011 07:00:46 -0600
Sergio Manzetti  wrote:

> Dear users, I have installed FFTW3 successfully, and confirmed its
> location using locate:
> 
> 
> However, when I try installing Gromacs 4.5.3 the -/configure step
> yields:
> 
> configure: error: Cannot find fftw3f library
> 
> 
> What am I doing incorrectly?

Looks like you're missing the development package. Run

# apt-get install libfftw3-dev

to fix this.
-- 
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jussi.leht...@helsinki.fi
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Re: [gmx-users] Ubuntu Installationync-mailbox>set editor=vim

2011-01-11 Thread Manuel Prinz

On Tue, Jan 11, 2011 at 07:00:46AM -0600, Sergio Manzetti wrote:
> Dear users, I have installed FFTW3 successfully, and confirmed its location
> using locate:

>From your output I assume you did so via APT?

> However, when I try installing Gromacs 4.5.3 the -/configure step yields:
> 
>   configure: error: Cannot find fftw3f library
> 
> What am I doing incorrectly?

apt-get install libfftw3-dev

(/usr/lib is already in the standard library search path, do not fiddle with
LDFLAGS and friends unless you really know what you are doing. It's almost
always the wrong solution to the problem.)

Best regards,
Manuel
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Re: [gmx-users] Ubuntu Installation

2011-01-11 Thread Bogdan Costescu

On Tue, Jan 11, 2011 at 14:19, Justin A. Lemkul  wrote:
>
>
> Sergio Manzetti wrote:
>>
>> Hi Justin, it was a blank ./configure

This defaults to something else than /usr/lib...

> I don't know why a standard location like /usr/lib isn't be detected as
> containing the libraries, but you can set LDFLAGS and CPPFLAGS accordingly
> so that the libraries and headers are found.  See the installation
> instructions for details.

Because the header files (.h) are also needed - there's none shown in
the list. Most likely the list contains files from a fftw package
installed with the distribution without the corresponding -devel
package.

Cheers,
Bogdan
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Re: [gmx-users] Ubuntu Installation

2011-01-11 Thread Justin A. Lemkul

Sergio Manzetti wrote:

Thanks,

so  LDFLAGS /home/user/gmx
and CPPFLAGS /home/user/gmx  for example?

Not quite.

./configure LDFLAGS="-L/usr/lib" CPPFLAGS="-I/usr/include" (presumably)

I still have no idea why configure wouldn't find these locations.

-Justin

On Tue, Jan 11, 2011 at 2:19 PM, Justin A. Lemkul > wrote:

Sergio Manzetti wrote:

Hi Justin, it was a blank ./configure

I don't know why a standard location like /usr/lib isn't be detected
as containing the libraries, but you can set LDFLAGS and CPPFLAGS
accordingly so that the libraries and headers are found.  See the
installation instructions for details.

-Justin

On Tue, Jan 11, 2011 at 2:03 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:

   Sergio Manzetti wrote:

   Dear users, I have installed FFTW3 successfully, and
confirmed
   its location using locate:

   /home/m/Desktop/gromacs-4.5.3/src/mdlib/gmx_fft_fftw3.c
   /usr/lib/libfftw3.so.3
   /usr/lib/libfftw3.so.3.2.4
   /usr/lib/libfftw3_threads.so.3
   /usr/lib/libfftw3_threads.so.3.2.4
   /usr/lib/libfftw3f.so.3
   /usr/lib/libfftw3f.so.3.2.4
   /usr/lib/libfftw3f_threads.so.3
   /usr/lib/libfftw3f_threads.so.3.2.4
   /usr/lib/libfftw3l.so.3
   /usr/lib/libfftw3l.so.3.2.4
   /usr/lib/libfftw3l_threads.so.3
   /usr/lib/libfftw3l_threads.so.3.2.4
   /usr/share/doc/libfftw3-3
   /usr/share/doc/libfftw3-3/NEWS.gz
   /usr/share/doc/libfftw3-3/README
   /usr/share/doc/libfftw3-3/README.Debian
   /usr/share/doc/libfftw3-3/changelog.Debian.gz
   /usr/share/doc/libfftw3-3/changelog.gz
   /usr/share/doc/libfftw3-3/copyright
   /var/cache/apt/archives/libfftw3-3_3.2.2-1_i386.deb
   /var/lib/dpkg/info/libfftw3-3.list
   /var/lib/dpkg/info/libfftw3-3.md5sums
   /var/lib/dpkg/info/libfftw3-3.postinst
   /var/lib/dpkg/info/libfftw3-3.postrm
   /var/lib/dpkg/info/libfftw3-3.shlib

   However, when I try installing Gromacs 4.5.3 the -/configure
   step yields:

   configure: error: Cannot find fftw3f library

   What am I doing incorrectly?

   Without seeing the command you gave to configure, it's
impossible to
   say.

   -Justin

   Sergio

   -- 

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.be

Re: [gmx-users] Ubuntu Installation

2011-01-11 Thread Sergio Manzetti

Thanks,

so  LDFLAGS /home/user/gmx
and CPPFLAGS /home/user/gmx  for example?

On Tue, Jan 11, 2011 at 2:19 PM, Justin A. Lemkul  wrote:

>
>
> Sergio Manzetti wrote:
>
>> Hi Justin, it was a blank ./configure
>>
>>
>>
> I don't know why a standard location like /usr/lib isn't be detected as
> containing the libraries, but you can set LDFLAGS and CPPFLAGS accordingly
> so that the libraries and headers are found.  See the installation
> instructions for details.
>
> -Justin
>
>
>> On Tue, Jan 11, 2011 at 2:03 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Sergio Manzetti wrote:
>>
>>Dear users, I have installed FFTW3 successfully, and confirmed
>>its location using locate:
>>
>>
>>/home/m/Desktop/gromacs-4.5.3/src/mdlib/gmx_fft_fftw3.c
>>/usr/lib/libfftw3.so.3
>>/usr/lib/libfftw3.so.3.2.4
>>/usr/lib/libfftw3_threads.so.3
>>/usr/lib/libfftw3_threads.so.3.2.4
>>/usr/lib/libfftw3f.so.3
>>/usr/lib/libfftw3f.so.3.2.4
>>/usr/lib/libfftw3f_threads.so.3
>>/usr/lib/libfftw3f_threads.so.3.2.4
>>/usr/lib/libfftw3l.so.3
>>/usr/lib/libfftw3l.so.3.2.4
>>/usr/lib/libfftw3l_threads.so.3
>>/usr/lib/libfftw3l_threads.so.3.2.4
>>/usr/share/doc/libfftw3-3
>>/usr/share/doc/libfftw3-3/NEWS.gz
>>/usr/share/doc/libfftw3-3/README
>>/usr/share/doc/libfftw3-3/README.Debian
>>/usr/share/doc/libfftw3-3/changelog.Debian.gz
>>/usr/share/doc/libfftw3-3/changelog.gz
>>/usr/share/doc/libfftw3-3/copyright
>>/var/cache/apt/archives/libfftw3-3_3.2.2-1_i386.deb
>>/var/lib/dpkg/info/libfftw3-3.list
>>/var/lib/dpkg/info/libfftw3-3.md5sums
>>/var/lib/dpkg/info/libfftw3-3.postinst
>>/var/lib/dpkg/info/libfftw3-3.postrm
>>/var/lib/dpkg/info/libfftw3-3.shlib
>>
>>
>>However, when I try installing Gromacs 4.5.3 the -/configure
>>step yields:
>>
>>configure: error: Cannot find fftw3f library
>>
>>
>>What am I doing incorrectly?
>>
>>
>>Without seeing the command you gave to configure, it's impossible to
>>say.
>>
>>-Justin
>>
>>Sergio
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] Ubuntu Installation

2011-01-11 Thread Justin A. Lemkul




Sergio Manzetti wrote:

Hi Justin, it was a blank ./configure




I don't know why a standard location like /usr/lib isn't be detected as 
containing the libraries, but you can set LDFLAGS and CPPFLAGS accordingly so 
that the libraries and headers are found.  See the installation instructions for 
details.


-Justin



On Tue, Jan 11, 2011 at 2:03 PM, Justin A. Lemkul > wrote:




Sergio Manzetti wrote:

Dear users, I have installed FFTW3 successfully, and confirmed
its location using locate:


/home/m/Desktop/gromacs-4.5.3/src/mdlib/gmx_fft_fftw3.c
/usr/lib/libfftw3.so.3
/usr/lib/libfftw3.so.3.2.4
/usr/lib/libfftw3_threads.so.3
/usr/lib/libfftw3_threads.so.3.2.4
/usr/lib/libfftw3f.so.3
/usr/lib/libfftw3f.so.3.2.4
/usr/lib/libfftw3f_threads.so.3
/usr/lib/libfftw3f_threads.so.3.2.4
/usr/lib/libfftw3l.so.3
/usr/lib/libfftw3l.so.3.2.4
/usr/lib/libfftw3l_threads.so.3
/usr/lib/libfftw3l_threads.so.3.2.4
/usr/share/doc/libfftw3-3
/usr/share/doc/libfftw3-3/NEWS.gz
/usr/share/doc/libfftw3-3/README
/usr/share/doc/libfftw3-3/README.Debian
/usr/share/doc/libfftw3-3/changelog.Debian.gz
/usr/share/doc/libfftw3-3/changelog.gz
/usr/share/doc/libfftw3-3/copyright
/var/cache/apt/archives/libfftw3-3_3.2.2-1_i386.deb
/var/lib/dpkg/info/libfftw3-3.list
/var/lib/dpkg/info/libfftw3-3.md5sums
/var/lib/dpkg/info/libfftw3-3.postinst
/var/lib/dpkg/info/libfftw3-3.postrm
/var/lib/dpkg/info/libfftw3-3.shlib


However, when I try installing Gromacs 4.5.3 the -/configure
step yields:

configure: error: Cannot find fftw3f library


What am I doing incorrectly?


Without seeing the command you gave to configure, it's impossible to
say.

-Justin

Sergio


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] Ubuntu Installation

2011-01-11 Thread Justin A. Lemkul




Sergio Manzetti wrote:
Dear users, I have installed FFTW3 successfully, and confirmed its 
location using locate:



/home/m/Desktop/gromacs-4.5.3/src/mdlib/gmx_fft_fftw3.c
/usr/lib/libfftw3.so.3
/usr/lib/libfftw3.so.3.2.4
/usr/lib/libfftw3_threads.so.3
/usr/lib/libfftw3_threads.so.3.2.4
/usr/lib/libfftw3f.so.3
/usr/lib/libfftw3f.so.3.2.4
/usr/lib/libfftw3f_threads.so.3
/usr/lib/libfftw3f_threads.so.3.2.4
/usr/lib/libfftw3l.so.3
/usr/lib/libfftw3l.so.3.2.4
/usr/lib/libfftw3l_threads.so.3
/usr/lib/libfftw3l_threads.so.3.2.4
/usr/share/doc/libfftw3-3
/usr/share/doc/libfftw3-3/NEWS.gz
/usr/share/doc/libfftw3-3/README
/usr/share/doc/libfftw3-3/README.Debian
/usr/share/doc/libfftw3-3/changelog.Debian.gz
/usr/share/doc/libfftw3-3/changelog.gz
/usr/share/doc/libfftw3-3/copyright
/var/cache/apt/archives/libfftw3-3_3.2.2-1_i386.deb
/var/lib/dpkg/info/libfftw3-3.list
/var/lib/dpkg/info/libfftw3-3.md5sums
/var/lib/dpkg/info/libfftw3-3.postinst
/var/lib/dpkg/info/libfftw3-3.postrm
/var/lib/dpkg/info/libfftw3-3.shlib


However, when I try installing Gromacs 4.5.3 the -/configure step yields:

configure: error: Cannot find fftw3f library


What am I doing incorrectly?



Without seeing the command you gave to configure, it's impossible to say.

-Justin


Sergio



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Ubuntu Installation

2011-01-11 Thread Sergio Manzetti

Dear users, I have installed FFTW3 successfully, and confirmed its location
using locate:


/home/m/Desktop/gromacs-4.5.3/src/mdlib/gmx_fft_fftw3.c
/usr/lib/libfftw3.so.3
/usr/lib/libfftw3.so.3.2.4
/usr/lib/libfftw3_threads.so.3
/usr/lib/libfftw3_threads.so.3.2.4
/usr/lib/libfftw3f.so.3
/usr/lib/libfftw3f.so.3.2.4
/usr/lib/libfftw3f_threads.so.3
/usr/lib/libfftw3f_threads.so.3.2.4
/usr/lib/libfftw3l.so.3
/usr/lib/libfftw3l.so.3.2.4
/usr/lib/libfftw3l_threads.so.3
/usr/lib/libfftw3l_threads.so.3.2.4
/usr/share/doc/libfftw3-3
/usr/share/doc/libfftw3-3/NEWS.gz
/usr/share/doc/libfftw3-3/README
/usr/share/doc/libfftw3-3/README.Debian
/usr/share/doc/libfftw3-3/changelog.Debian.gz
/usr/share/doc/libfftw3-3/changelog.gz
/usr/share/doc/libfftw3-3/copyright
/var/cache/apt/archives/libfftw3-3_3.2.2-1_i386.deb
/var/lib/dpkg/info/libfftw3-3.list
/var/lib/dpkg/info/libfftw3-3.md5sums
/var/lib/dpkg/info/libfftw3-3.postinst
/var/lib/dpkg/info/libfftw3-3.postrm
/var/lib/dpkg/info/libfftw3-3.shlib


However, when I try installing Gromacs 4.5.3 the -/configure step yields:

configure: error: Cannot find fftw3f library


What am I doing incorrectly?

Sergio
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[gmx-users] Re: question on implicit membrane in gromacs

2011-01-11 Thread David van der Spoel


On 2011-01-11 12.36, Simon Ágnes wrote:

Dear dr. van der Spoel,

I am wondering whether it is possible to perform molecular dynamics in
Gromacs with implicit membrane.

(I searched the mailing list archive and I guess that it is not
possible, but I would like to make sure, whether my information is correct).

Kind regards,

Agnes Simon, Ph.D

Chemical Research Center,

Budapest, Hungary


It is not implemented, but would not be very difficult to do.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Problem with COM movement

2011-01-11 Thread Tomy van Batis

Dear all

I have the following system:

Two substrates (which are FCC lattices consisting of LJ particles) in a
distance of 50nm and between these substrates I put completely stretched
polymer chains. The substrates are parallel to xy plane and the chains are
vertical. The length of the stretched chains is 30 nm and I put them in the
middle, so the distance of the each substrate to be 10nm.  The interaction
between the substrates and the polymers is repulsive and it’s the same for
each substrate.

I want my substrates to be stable during the simulation, but to be able also
to move under compression (in the z axis).

For that purpose in my .mdp file I define the following:

*nstcomm  = 1*

*comm-grps= ZZZ   **,where ZZZ is the name of the residue of
the substrates*

* *

I have 2 problems:

1)  At the beginning, I run NVT for 20ns and the chains are moving UP
during the simulation.

Since my system is completely symmetric, I would expect to have symmetric
movement of the chains, i.e. symmetric density profile.



2)  In my .log file the following message appears:

*Large VCM(group rest):  0.0, -0.0,  0.1,
T-cm:
inf*

It doesn’t appear as an error message, but it appears thousand times in my
log file. I had a look in the mailing list about that, but I did not find a
proper answer.



Can anyone help me?



I also have one question:

When I remove that COM motion of one residue, i.e. from the ZZZ (by adding
comm grps: ZZZ in my mdp file), what happening with the COM motion of the
rest of the system?



I hope I was clear!



Thanks in advance, Chrysostomos
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RE: [gmx-users] truncated LJ potential

2011-01-11 Thread Berk Hess


Yes.

The pow function is expensive though. The code will run much faster
if you can use rinvsix, such as check for  2*rinvsix > c6/c12.
(I forgot the factor 2 in my previous mail).

Berk

> From: makoto-yon...@aist.go.jp
> To: gmx-users@gromacs.org
> Date: Tue, 11 Jan 2011 10:10:56 +0900
> Subject: [gmx-users] truncated LJ potential
> 
> Dear Berk:
> 
> Thanks again for the further reply.
> 
> >> The LJ potential and force code in the above looks like in the c6-c12
> form
> >> not in epsilon-sigma one.
> >> The LJ potential modification I'd like to try is based on the epsilon-
> >> sigma form and the mixing rule is the Lorents-Bertelot's one.
> >> Could you kindly tell me the LJ potential and force routine in the
> epsilon-
> >> Sigma form.
> >
> >There is no such code.
> >
> >You can simply check for rinvsix > c6/c12
> 
> Is it means that the LJ potential in epsion-sigma form (with the
> Lorents-Bertelot 
> mixing rule) is evaluated after the coversion into c6-c12 form in GROMACS?
> Then, may I evaluate the modified LJ potential:
> 
> > > V(r)
> > >= 4*epsilon*{ (sigma/r)^(12) - (sigma/r)^6 + (1/4) } for r<=
> > > 2^(1/6)*sigma
> > >= 0 for r>  2^(1/6)*sigma
> 
> with translated into the equivalent c6-c12 form:
> 
> V(r)
>= (c12/r)^(12) - (c6/r)^6 + (c6/2)*(c6/2*c12) for r<= (2*c12/c6)^(1/6)
>= 0 for r > (2*c12/c6)^(1/6)
> 
> in the following routines.
> > > You can also set the environment variable nb_generic.c and modify
> > > src/gmxlib/nonbonded/nb_generic.c, but might lead to somewhat
> > > slower simulations.
> 
> If my understanding in the above would correct, I'll try that.
> 
> Thank you for advance.
> 
> Makoto Yoneya, Dr.
> http://staff.aist.go.jp/makoto-yoneya/
> 
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