Re: [gmx-users] differentiate color of molecules

2008-10-23 Thread Mark Abraham 

 huan wrote:

Dear all gms-users and developers,

I have 6 types of molecules in my system. So, when i view the pdb file 
(results) using Rasmol, i cannot differentiate the molecules by their colors. 
Any suggestions for me to have a better way to differentiate the molecules?


I don't know about Rasmol. It's easy to do such things with VMD, which I 
recommend heartily. You might be better served asking a Rasmol list if 
you're only prepared to use it.


Mark
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[gmx-users] differentiate color of molecules

2008-10-23 Thread hhhh huan 
Dear all gms-users and developers,

I have 6 types of molecules in my system. So, when i view the pdb file 
(results) using Rasmol, i cannot differentiate the molecules by their colors. 
Any suggestions for me to have a better way to differentiate the molecules?


Thanks


  
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[gmx-users] workshop

2008-10-23 Thread hhhh huan 
Dear all.

What is the procedure if we ( my research group) want to organize a workshop at 
my University?

Thanks


  
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Re: [gmx-users] Unary Diez Operator error while compiling gromacs 4.0

2008-10-23 Thread Mark Abraham 

[EMAIL PROTECTED] wrote:

Hello,

I am having difficulty compiling gromacs 4.0 on an Itanium2 running HP 
Linux XC 3.0.


Gromacs 3.3.1 compiled fine on that machine. I have successfully 
compiled gromacs 4.0 this way on opterons running HP Linux XC 3.2.1 and 
HP Linux XC 3.1.


I have seen a post in the archives showing a slightly different initial 
error that eventually leads to "Unexpected token: Unary Diez Operator 
at: Start" for gromacs 3.3.2, but assumed that any such fix would have 
been incorporated into gromacs 4.0.


Still, I tried that solution 
(http://www.gromacs.org/pipermail/gmx-users/2007-October/030212.html) 
but it did not work, possibly because I am unclear what directory I 
should execute the command from:


That discussion wasn't ever satisfactorily resolved. On the same machine 
 on which I reported the above, I also failed to compile GROMACS 4.0 
using the Intel 9.1 compilers. The error messages were the same kind as 
before, though I didn't compare in detail.


I succeeded in compiling GROMACS 4.0 on this machine with

module load scsl
module load intel-cc/10.1.018
module load fftw/3.1.1-intel-9.1
../configure --program-suffix=_mpi_c CC=icc CFLAGS="-O3 
-I${FFTWDIR}/include" LIBS="-L${FFTWDIR}/lib -lscs -lmpi" --prefix 
${HOME}/progs --with-external-blas --with-external-lapack 
--with-fft=fftw3 --enable-mpi --without-x

make mdrun

This suggests there's an issue with the Intel 9.1 compilers.

[EMAIL PROTECTED] gromacs-4.0]$ icc -DHAVE_CONFIG_H -I. -I../../../../src 
-I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double 
-I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" 
-O0 -w -MT nb_kernel010_ia64_double.lo -MD -MP -MF 
.deps/nb_kernel010_ia64_double.Tpo -E 
../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S 
-fPIC -DPIC -o temp.s
cpp: 
../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S: 
No such file or directory

cpp: warning: `-x assembler-with-cpp' after last input file has no effect
cpp: no input files


I see you've copied my icc command from October. I was creating a 
subdirectory under GROMACS 4.0 so that I could maintain separate build 
trees for different compilation options, e.g.


mkdir mpi
cd mpi
../configure --enable-mpi
cd ..
mkdir nonmpi
cd nonmpi
../configure
cd ..

etc. This means I don't have to make distclean all the time, and can 
know the state of each subdirectory when I return to it after some time. 
You can also do this while experimenting over a range of compiler 
optimization flags.


You should harvest your own from the make output just before it fails.

Mark
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Re: [gmx-users] f(x) g(x) h(x)in the user defined potential functions

2008-10-23 Thread Mark Abraham 

He, Yang wrote:

Hi all users,

When I am defining the user potential functions using the table, I encountered a problem 
that there are several unstable parameters  in the separate f(x),g(x),h(x) .For example, 
in the g(x), there is a parameter "epsilon" whose value will depend on 
different pairs.In this situation, I can not get a specific value in the table file . I 
don't know how to solve this problem.

Can anyone of you give me some suggestions about that?


So your nonbonded interaction depends on your atom types. You could 
write a table for each interaction type, modify GROMACS to read them all 
in, and then modify the routine that calls the kernels to use the 
correct one. This additional memory usage would grow as the square of 
the number of atom types. You would also see some performance loss which 
you could minimize by arranging to evaluate all of one type of nonbonded 
interaction close together in the nonbonded routines, to minimize cache 
misses.


Better would be if some of these functions (conveniently) differed only 
by a multiplicative or additive constant so that you could re-use the 
same table and then apply a correction function, but you'll have to look 
at your own maths for that.


Mark
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[gmx-users] f(x) g(x) h(x)in the user defined potential functions

2008-10-23 Thread He, Yang 
Hi all users,

When I am defining the user potential functions using the table, I encountered 
a problem that there are several unstable parameters  in the separate 
f(x),g(x),h(x) .For example, in the g(x), there is a parameter "epsilon" whose 
value will depend on different pairs.In this situation, I can not get a 
specific value in the table file . I don't know how to solve this problem.

Can anyone of you give me some suggestions about that?

Thank you in advance.

Yang
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RE: [gmx-users] stochastic dynamics , langevin

2008-10-23 Thread Matthew Hoopes 
Along these same lines...
(a)is there an thermostat setting in GROMACS that comes close to the DPD
thermostat as described in (T. Soddemann, B. D¨unweg, and K. Kremer.
Dissipative particle dynamics: A useful thermostat for equilibrium and
nonequilibrium molecular dynamics simulations. Phys. Rev. E, 68:046702,
2003.)
(b) if nothing approaches DPD, how would a one go about starting to write a
new thermostat in GROMACS?

-Matt

-
Matthew Hoopes
Biophysics Graduate Group
University of California, Davis

[EMAIL PROTECTED]
530-752-6452
- 


Hi,

Brownina dynamics is a Langevin equation for the coordinates (no inertia).
Stochastic dynamics is a Langevin equation for the velocities (with
inertia).

Everything depends on what you want to do, which you do not tell in detail.
If you want to leave out the solvent, but you want to simulate a system in
solvent, SD is not going to help you, since there is no implicit solvent
potential, so your potential and therefore your sampling is nonsense.

tau_t has no effect on the distribution, only on the dynamics. If you want
the correct dynamics, you will have fit tau_t to reproduce some kinetic
quantity that you are interested in. For different quantities tau_t can be
different.

Berk


Date: Thu, 23 Oct 2008 15:31:16 +0200
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] stochastic dynamics , langevin

Dear All,
I am trying to perform Langevin dynamics of large peptides / proteins. After
reading the manual & going over some old mails in this list, I have two
points I hope you could clear for me:

[Gromacs version 3.3.3]

1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the
proper keywords I should use for Langevin dynamics: integrator = sd ;

bd-fric= 0 ;
tau_t  = 10 ;
ref_t  = 300 ;
With bd-fric=0, the friction is taken as the inverse tau_t.


2) From your experience, what are good values of tau_t (or 1/tau_t) for
simulating a protein? In 2006 list, David has commented that choosing tau_t
is very important (
http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ).


Your help is appreciated. Omer.  
Koby Levy research group,
Weizmann Institute of Science. 
http://www.weizmann.ac.il/sb/faculty_pages/Levy/

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[gmx-users] Unary Diez Operator error while compiling gromacs 4.0

2008-10-23 Thread chris . neale 

Hello,

I am having difficulty compiling gromacs 4.0 on an Itanium2 running HP  
Linux XC 3.0.


Gromacs 3.3.1 compiled fine on that machine. I have successfully  
compiled gromacs 4.0 this way on opterons running HP Linux XC 3.2.1  
and HP Linux XC 3.1.


I have seen a post in the archives showing a slightly different  
initial error that eventually leads to "Unexpected token: Unary Diez  
Operator at: Start" for gromacs 3.3.2, but assumed that any such fix  
would have been incorporated into gromacs 4.0.


Still, I tried that solution  
(http://www.gromacs.org/pipermail/gmx-users/2007-October/030212.html)  
but it did not work, possibly because I am unclear what directory I  
should execute the command from:


[EMAIL PROTECTED] gromacs-4.0]$ icc -DHAVE_CONFIG_H -I. -I../../../../src  
-I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double  
-I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\"  
-O0 -w -MT nb_kernel010_ia64_double.lo -MD -MP -MF  
.deps/nb_kernel010_ia64_double.Tpo -E  
../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S -fPIC -DPIC -o  
temp.s
cpp:  
../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S: No such file or  
directory

cpp: warning: `-x assembler-with-cpp' after last input file has no effect
cpp: no input files

--then--

[EMAIL PROTECTED] gromacs-4.0]$ icc -DHAVE_CONFIG_H -I. -I./src  
-I./src/gmxlib/nonbonded/nb_kernel_ia64_double -I./include  
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O0 -w -MT  
nb_kernel010_ia64_double.lo -MD -MP -MF  
.deps/nb_kernel010_ia64_double.Tpo -E  
./src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S -fPIC  
-DPIC -o temp.s
./src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S:0:  
fatal error: opening dependency file  
.deps/nb_kernel010_ia64_double.Tpo: No such file or directory

compilation terminated.

--then--

$cd /work/cneale/exe/gromacs-4.0/src/gmxlib/nonbonded/nb_kernel_ia64_double
[EMAIL PROTECTED] nb_kernel_ia64_double]$ icc -DHAVE_CONFIG_H -I.  
-I../../../../src  
-I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double  
-I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\"  
-O0 -w -MT nb_kernel010_ia64_double.lo -MD -MP -MF  
.deps/nb_kernel010_ia64_double.Tpo -E  
../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S -fPIC -DPIC -o  
temp.s
cpp:  
../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S: No such file or  
directory

cpp: warning: `-x assembler-with-cpp' after last input file has no effect
cpp: no input files

#

The compile script was like this:

#!/bin/bash

MD=/work/cneale/exe/gromacs-4.0
cd ${MD}
mkdir exec

export FFTW_LOCATION=/work/cneale/exe/fftw-3.1.2/exec
export GROMACS_LOCATION=${MD}/exec
export CPPFLAGS=-I$FFTW_LOCATION/include
export LDFLAGS=-L$FFTW_LOCATION/lib

./configure --prefix=$GROMACS_LOCATION --without-motif-includes
make
make install
make distclean

###

And here is the first error reported by make (which turn out to be fatal):
make[5]: Entering directory  
`/work/cneale/exe/gromacs-4.0/src/gmxlib/nonbonded/nb_kernel_ia64_single'
source='nb_kernel010_ia64_single.S'  
object='nb_kernel010_ia64_single.lo' libtool=yes \

DEPDIR=.deps depmode=gcc /bin/sh ../../../../config/depcomp \
/bin/sh ../../../../libtool   --mode=compile cc -DHAVE_CONFIG_H -I.  
-I../../../../src -I/usr/X11R6/include -I/usr/include/libxml2  
-I../../../../include  
-DGMXLIBDIR=\"/work/cneale/exe/gromacs-4.0/exec/share/top\"  
-I/work/cneale/exe/fftw-3.1.2/exec/include  -O3 -w -c -o  
nb_kernel010_ia64_single.lo nb_kernel010_ia64_single.S
 cc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/X11R6/include  
-I/usr/include/libxml2 -I../../../../include  
-DGMXLIBDIR=\"/work/cneale/exe/gromacs-4.0/exec/share/top\"  
-I/work/cneale/exe/fftw-3.1.2/exec/include -O3 -w -c  
nb_kernel010_ia64_single.S -Wp,-MD,.deps/nb_kernel010_ia64_single.TPlo  
-o nb_kernel010_ia64_single.o
/tmp/iccMZaG8n.s(1) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(2) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(3) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(4) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(5) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(6) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(7) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(8) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(10) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(15) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(193) : error A2040: Unexpected token: Unary Diez  
Operator at: Start
/tmp/iccMZaG8n.s(195) : e

RE: [gmx-users] how to use the new potential

2008-10-23 Thread He, Yang 
Hi Mark,

Thank you for your reply. I will follow your suggestions and have a try.

Hope to get further help

Regards,

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Matthew Hoopes [EMAIL 
PROTECTED]
Sent: Wednesday, October 22, 2008 5:41 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] how to use the new potential

>He, Yang wrote:
>> Hi all users,
>>
>> I am engaged in deal with the course grain model,in which the
>> potential functions are not the same as in gromacs.Hence, If I want to
>> use the new potentials , I guess I can change the source code or use
>> the table. But I never have this experience about  that.Can anyone of
>> you give me some suggestions or examples?
>
>Start with the manual. :-) Hopefully the version 4 manual will be out
>soon, but even if not, the 3.3 manual will be fine for nonbonded
>tabulated potentials.
>
>Mark

Here is an example:

#
# Tabulated WCA potentials, dr=0.002, rc=3.5, no coulomb
#
0.00e+00  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
2.00e-03  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
...
3.60e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
3.80e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
4.00e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  2.3841857812e+17  7.1525573584e+19
4.20e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  1.3276038530e+17  3.7931538762e+19
4.40e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  7.5967506265e+16  2.0718410875e+19
4.60e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  4.4562136749e+16  1.1624905294e+19
...
3.498000e+00  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
3.50e+00  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00

Column 1) is r (distance between atoms) 6) h(r) the repulsive term of the
potential and 7) -h'(r) as defined in section 6.7.2

1) Just use your favorite script (I used octave) to generate the following
text file with printf statements or something similar.
2) If some of the early values are too large, it may cause an error so I
just zeroed them out.
3) The information you need is in a few places in the manual. The table
above is defined in section 6.7.2 on page 131 of the GROMACS 4.0 manual.
4) You will also want to read section 7.3.12 on page 148 about entries in
your parameter file (e.g. energy groups, table file naming conventions)
5) You will need an index file that has particle groups for your new
potentials. The group names in the index file are what you use for energy
groups.
6) Pay attention to which combination rules you use in the topology file
7) Note that in the LJC(12-6-1) table in the top directory of GROMACS, the
minimum of the LJ is -0.25 and not -1.0 so I guess there is a factor of
4*epsilon multiplied to the table values.

What I don't know, and perhaps someone else can answer this is what should
be done if you are unsure of how your potential is separated in to
attractive and repulsive terms (e.g. LJ with COS tail). First, it's
piecewise, and second the COS section is not the sum of two terms so how
should it be broken across g(r) and h(r) or is it always OK to use the g(r)
column for the whole potential?

Hope this helps.

-Matt

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Re: [gmx-users] stochastic dynamics , langevin

2008-10-23 Thread Suman Chakrabarty 
Berk Hess wrote:
> Everything depends on what you want to do, which you do not tell in detail.
> If you want to leave out the solvent, but you want to simulate a system
> in solvent,
> SD is not going to help you, since there is no implicit solvent potential,
> so your potential and therefore your sampling is nonsense.


So can we assume that the sampling is equivalent to that in vacuum (as
far as underlying potential/free energy surface is concerned), with only
the dynamics being slowed down by the viscous drag?

Also, is it a safe guideline to use Langevin dynamics for small
particles in not so viscous fluid and Brownian dynamics for large
particles in highly viscous fluid?


Regards,
Suman.


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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RE: [gmx-users] PCA comparison

2008-10-23 Thread Berk Hess 
Hi,

The message from all your analysis is very clear:
Your principal components have not converged.

Berk.

> Date: Thu, 23 Oct 2008 14:37:00 +
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] PCA comparison
> 
> 
> Hi Berk,
> Indeed, when I say that the overlap is below 0.4 I mean the highest
> values of the matrix of inner products. I expected the vectors to be
> quite similar with their neighbours, i.e. I expected vector 5 to have a
> high inner product with 5, or 4 or 6 of the other set. But this diagonal
> trend, although present, is very weak, and is in fact more present for
> the lower pc that the higher!
> A part from the cosine content, we have checked the projections  of the
> trajectory, and except for the 1st and 2nd pc's, the other exhaustively
> oscillate around the mean value, which I though indicated good sampling.
> Otherwise, how can I asses if the PCA makes any sense? (there are papers
> that do PCA with shorter trajectories...)
> Thanks!
> Ramon
> 
> 
> 
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[gmx-users] PCA comparison

2008-10-23 Thread rcsqtc 

Hi Berk,
Indeed, when I say that the overlap is below 0.4 I mean the highest
values of the matrix of inner products. I expected the vectors to be
quite similar with their neighbours, i.e. I expected vector 5 to have a
high inner product with 5, or 4 or 6 of the other set. But this diagonal
trend, although present, is very weak, and is in fact more present for
the lower pc that the higher!
A part from the cosine content, we have checked the projections  of the
trajectory, and except for the 1st and 2nd pc's, the other exhaustively
oscillate around the mean value, which I though indicated good sampling.
Otherwise, how can I asses if the PCA makes any sense? (there are papers
that do PCA with shorter trajectories...)
Thanks!
Ramon



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Re: [gmx-users] stochastic dynamics , langevin

2008-10-23 Thread Omer Markovitch 
Thanks for the quick reply Berk.


>
> 1) Is this the proper keywords I should use for Langevin dynamics:
> integrator = sd ;
> bd-fric= 0 ;
> tau_t  = 10 ;
> ref_t  = 300 ;
>

Basically, I want to know if I am using the 4 parameters correctly.
That is - for Langevin dynamics, I should pick bd-fric=0, to allow the
friction to be taken from 1/tau_t ?
Secondly, I am looking for examples of tau_t different people use for
different system.
Thanks, Omer.
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Re: [gmx-users] I want to write the acetaldehyde topology files

2008-10-23 Thread Justin A. Lemkul 



Jinyao Wang wrote:

Hi,
 I want to carry out acetaldehyde simulation with OPLS-AA. However, I am not 
able to write the acetaldehyde topology files. If someone could sent me some 
materials aboult OPLS-AA for acetaldehyde, I would very appreciate it.



So why are you unable to write the topology?  Chapter 5 of the manual explains 
how to do it, and for a molecule like acetaldehyde it should be quite 
straightforward.


-Justin




致
礼！


Jinyao Wang
[EMAIL PROTECTED]
　　2008-10-23




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--


Justin A. Lemkul
Graduate Research Assistant
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] I want to write the acetaldehyde topology files

2008-10-23 Thread Jinyao Wang 
Hi,
 I want to carry out acetaldehyde simulation with OPLS-AA. However, I am not 
able to write the acetaldehyde topology files. If someone could sent me some 
materials aboult OPLS-AA for acetaldehyde, I would very appreciate it.



致
礼！


Jinyao Wang
[EMAIL PROTECTED]
　　2008-10-23
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RE: [gmx-users] stochastic dynamics , langevin

2008-10-23 Thread Berk Hess 
Hi,

Brownina dynamics is a Langevin equation for the coordinates (no inertia).
Stochastic dynamics is a Langevin equation for the velocities (with inertia).

Everything depends on what you want to do, which you do not tell in detail.
If you want to leave out the solvent, but you want to simulate a system in 
solvent,
SD is not going to help you, since there is no implicit solvent potential,
so your potential and therefore your sampling is nonsense.

tau_t has no effect on the distribution, only on the dynamics.
If you want the correct dynamics, you will have fit tau_t to
reproduce some kinetic quantity that you are interested in.
For different quantities tau_t can be different.

Berk


Date: Thu, 23 Oct 2008 15:31:16 +0200
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] stochastic dynamics , langevin

Dear All,
I am trying to perform Langevin dynamics of large peptides / proteins.
After reading the manual & going over some old mails in this list, I have two 
points I hope you could clear for me:

[Gromacs version 3.3.3]

1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the proper 
keywords I should use for Langevin dynamics:
integrator = sd ;

bd-fric= 0 ;
tau_t  = 10 ;
ref_t  = 300 ;
With bd-fric=0, the friction is taken as the inverse tau_t.


2) From your experience, what are good values of tau_t (or 1/tau_t) for 
simulating a protein? In 2006 list, David has commented that choosing tau_t is 
very important ( 
http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ).


Your help is appreciated. Omer.  
Koby Levy research group,
Weizmann Institute of Science. 
http://www.weizmann.ac.il/sb/faculty_pages/Levy/




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[gmx-users] stochastic dynamics , langevin

2008-10-23 Thread Omer Markovitch 
Dear All,
I am trying to perform Langevin dynamics of large peptides / proteins.
After reading the manual & going over some old mails in this list, I have
two points I hope you could clear for me:
[Gromacs version 3.3.3]

1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the
proper keywords I should use for Langevin dynamics:
integrator = sd ;
bd-fric= 0 ;
tau_t  = 10 ;
ref_t  = 300 ;
With bd-fric=0, the friction is taken as the inverse tau_t.

2) From your experience, what are good values of tau_t (or 1/tau_t) for
simulating a protein? In 2006 list, David has commented that choosing tau_t
is very important (
http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ).

Your help is appreciated. Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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[gmx-users] amber and vsites

2008-10-23 Thread Erik Marklund 

Hi,

I'm trying to get vsites working for my DNA decamer with ffamber03. I've 
added the following to ffamber03.ddb,


[ NH2 ]
; N2-CA in Adenosine/Guanine
amber99_38 planar

but pdb2gmx adds no virtual sites to the adenosines/guanines. What am I 
missing here?


--
---
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] nanoparticle-protein simulation

2008-10-23 Thread jahanshah ashkani 
Hi there,
I would be glad if somebody let me know how I can simulate a 
Nanoparticle-protein complex by GROMACS.
Thank you very much.

Best,
J

Jahanshah Ashkani,

PhD student of Biotechnology & Genetics,

University of the Western Cape,

Biotechnology Department,

Private Bag X17,

7735 Bellville,

Cape Town,

South Africa

[EMAIL PROTECTED]

--- On Thu, 10/23/08, Abu Naser <[EMAIL PROTECTED]> wrote:
From: Abu Naser <[EMAIL PROTECTED]>
Subject: RE: [gmx-users] spliting clusters.pdb
To: "Discussion list for GROMACS users" 
Date: Thursday, October 23, 2008, 5:08 AM




#yiv1368626862 .hmmessage P
{
margin:0px;padding:0px;}
#yiv1368626862 {
FONT-SIZE:10pt;FONT-FAMILY:Tahoma;}


Hi Jochen,

 

Thanks for your replay. I manage to do that using trjconv. However, I will keep 
your

suggestion in my mind for future use.









 

> Date: Wed, 22 Oct 2008 18:04:01 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] spliting clusters.pdb
> 
> Abu Naser wrote:
> > Hi All,
> > 
> > I have been wondering whether there is any tools for spliting clusters.pdb 
> > file into individual snapshots.
> 
> If there is a TER between the structures, the shell command csplit may
> be useful for you.
> 
> Jochen
> 
> 
> > 
> > With regards,
> > 
> > Abu
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _
> > Win an Xbox 360 or £200 Top Shop Vouchers 
> > http://clk.atdmt.com/GBL/go/115454062/direct/01/
> > 
> > 
> > 
> > 
> > ___
> > gmx-users mailing list gmx-users@gromacs.org
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> > www interface or send it to [EMAIL PROTECTED]
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> 
> 
> -- 
> 
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
> 
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RE: [gmx-users] spliting clusters.pdb

2008-10-23 Thread Abu Naser 

Hi Jochen,
 
Thanks for your replay. I manage to do that using trjconv. However, I will keep 
your
suggestion in my mind for future use.






 > Date: Wed, 22 Oct 2008 18:04:01 +0200> From: [EMAIL PROTECTED]> To: 
 > gmx-users@gromacs.org> Subject: Re: [gmx-users] spliting clusters.pdb> > Abu 
 > Naser wrote:> > Hi All,> > > > I have been wondering whether there is any 
 > tools for spliting clusters.pdb file into individual snapshots.> > If there 
 > is a TER between the structures, the shell command csplit may> be useful for 
 > you.> > Jochen> > > > > > With regards,> > > > Abu> > > > > > > > > > > > > 
 > > > > _> > 
 > Win an Xbox 360 or £200 Top Shop Vouchers > > 
 > http://clk.atdmt.com/GBL/go/115454062/direct/01/> > > > > > 
 > > > 
 > > > ___> > gmx-users mailing 
 > list gmx-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> > > -- > 
 > > Dr. Jochen Hub> Max Planck 
 > Institute for Biophysical Chemistry> Computational biomolecular dynamics 
 > group> Am Fassberg 11> D-37077 Goettingen, Germany> Email: jhub[at]gwdg.de> 
 > Tel.: +49 (0)551 201-2312> > 
 > ___> gmx-users mailing list 
 > gmx-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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Re: [gmx-users] monomer's conectivity

2008-10-23 Thread Andrea Muntean 
It did work. Thank you!

Cheers,
Andrea

2008/10/23 Mark Abraham <[EMAIL PROTECTED]>

> Andrea Muntean wrote:
>
>> Thank you for your answer.
>>  If I am looking at the PDB standard format and my file, I observe that I
>> have only one number between the type of residue and coordinates, and I
>> suppose it is the residue current number. I am indeed missing the chain
>> identifier code, which should be of A1 Fortran format, which I don't really
>> understand (one carachter, but I have 32 chains, so it should be minimum A2
>> or I2). That I could introduce.
>>
>
> Get a PDB file with just one polymer molecule and work on getting a
> topology for that. Walking before running :-)
>
> In my pdb entries I dont define any connectors. Should they be a dummy
>> atom, with the corresponding bond, angle, dihedhral, which after that I
>> redefine in the tdb file?
>>
>
> First you need a functional *residue topology*. Check chapter 5 of the
> manual and look at the other force fields to see how (for example) protein
> force fields define the connectors with + and - prefixes. Once you've got
> that, then it's possible for pdb2gmx to join them head to tail (using the
> residue number field to indicate the breaks, and the name to match up with
> the topology you've defined), and you may then need either terminating
> residues of a different name or a .tdb entry.
>
> I dont think it is a visualisation artefact, because it really gives less
>> number of bonds, corresponding to the missing intermonomeric bonds.
>>
>
> Your visualization software is not reading a file format that is encoding
> any topology (since you haven't produced one yet). Thus it's inventing some
> bonds based on the coordinates. The output of pdb2gmx that contains topology
> information is the .top file, not the coordinate file.
>
> Should I do now both (introducing a chain identifier in the pdb, but how?,
>> and defining the intermonomeric bonds via dummy in the pdb and tdb?)?
>>
>
> I suppose there are some circumstances where chain identifiers might be
> useful, but since you haven't even told us what your monomer and system are,
> it's hard to help you.
>
>
> Mark
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RE: [gmx-users] PCA comparison

2008-10-23 Thread Berk Hess 
Hi,

The cosine content can only be use for "negative" conclusions.
If it is high, the sampling is bad.
If it is low, the sampling can be either good or bad, it doesn't tell.

The overlap is a much better measure.
Since it is so low, you have bad sampling.

Have you looked at the eigenvector inner products to check
if the pc directions change, or if only the eigenvalue change?

Berk

> Date: Thu, 23 Oct 2008 13:10:23 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] PCA comparison
> 
> Dear all,
> We are performing some PCA analysis of several 22ns trajectories of a
> protein hexamer at different temperatures (280, 300, 320K). We expected
> to see a similar movement decribed by the ~10 lowest PCA's.
> their overlap is very poor: Below 0.35, and the diagonal elements are
> not remarkably higher than the rest. If we split one of the trajectories
> into to 11ns ones and do the same, again the overlap obtained is below
> 0.44 in all cases and there is no clear diagonal. 11ns is quite a long
> trajectory so I expected to see the same type of movement described by
> both 11ns fragments. Here are the cosine contents of the whole 22 ns
> trajectory and the two fragments. Except for the 1st pc, the rest seem
> well sampled: shouldn't they agree?
> 22ns:
> Cosine content  PC1 0.956255
> Cosine content  PC2 0.00428106
> Cosine content  PC3 0.000162083
> 
> 1st 11ns:
> Cosine content  PC1 0.923261
> Cosine content  PC2  0.0217681
> Cosine content  PC3 0.0135543
> 
> 2nd 11ns:
> Cosine content  PC1 0.786694
> Cosine content  PC2 0.1654
> Cosine content  PC3 0.000335589
> 
> Are we doing something wrong? Is this the exptected behaviour?
> This is what we do to calculate the PCA's (10ns of equilibration removed):
> g_covar -f trajectory.xtc -b 1 -e 21000 -s structure.pdb -o
> eigenval-T300-A.xvg -v eigenvec-T300-A.trr -av average-pca-T300-A.pdb
> g_covar -f trajectory.xtc -b 21020 -s structure.pdb -o
> eigenval-T300-B.xvg -v eigenvec-T300-B.trr -av average-pca-T300-B.pdb
> 
> and to compare them:
> g_anaeig -inpr T300-A-B.xpm -v eigenvec-T300-A.trr -v2
> eigenvec-T300-B.trr -first 1 -last 10
> 
> Thanks for your help and suggestions!
> Ramon
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Re: [gmx-users] monomer's conectivity

2008-10-23 Thread Justin A. Lemkul 



Andrea Muntean wrote:

Thank you. I hope this helps me further.
My system is 32 polystyrene chains of 80 monomers.


Mark's suggestion about generating an .rtp entry is a good one for your 
purposes, then.  Also search the list archive for "polymer" or "polystyrene" and 
you will find many pertinent discussions involving people who have done what you 
need to do, and the problems they faced along the way.


-Justin


Andrea
2008/10/23 Mark Abraham <[EMAIL PROTECTED] 
>


Andrea Muntean wrote:

Thank you for your answer.
 If I am looking at the PDB standard format and my file, I
observe that I have only one number between the type of residue
and coordinates, and I suppose it is the residue current number.
I am indeed missing the chain identifier code, which should be
of A1 Fortran format, which I don't really understand (one
carachter, but I have 32 chains, so it should be minimum A2 or
I2). That I could introduce.


Get a PDB file with just one polymer molecule and work on getting a
topology for that. Walking before running :-)


In my pdb entries I dont define any connectors. Should they be a
dummy atom, with the corresponding bond, angle, dihedhral, which
after that I redefine in the tdb file?


First you need a functional *residue topology*. Check chapter 5 of
the manual and look at the other force fields to see how (for
example) protein force fields define the connectors with + and -
prefixes. Once you've got that, then it's possible for pdb2gmx to
join them head to tail (using the residue number field to indicate
the breaks, and the name to match up with the topology you've
defined), and you may then need either terminating residues of a
different name or a .tdb entry.


I dont think it is a visualisation artefact, because it really
gives less number of bonds, corresponding to the missing
intermonomeric bonds.


Your visualization software is not reading a file format that is
encoding any topology (since you haven't produced one yet). Thus
it's inventing some bonds based on the coordinates. The output of
pdb2gmx that contains topology information is the .top file, not the
coordinate file.


Should I do now both (introducing a chain identifier in the pdb,
but how?, and defining the intermonomeric bonds via dummy in the
pdb and tdb?)?


I suppose there are some circumstances where chain identifiers might
be useful, but since you haven't even told us what your monomer and
system are, it's hard to help you.


Mark
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] PCA comparison

2008-10-23 Thread Ramon Crehuet 
Dear all,
We are performing some PCA analysis of several 22ns trajectories of a
protein hexamer at different temperatures (280, 300, 320K). We expected
to see a similar movement decribed by the ~10 lowest PCA's.
their overlap is very poor: Below 0.35, and the diagonal elements are
not remarkably higher than the rest. If we split one of the trajectories
into to 11ns ones and do the same, again the overlap obtained is below
0.44 in all cases and there is no clear diagonal. 11ns is quite a long
trajectory so I expected to see the same type of movement described by
both 11ns fragments. Here are the cosine contents of the whole 22 ns
trajectory and the two fragments. Except for the 1st pc, the rest seem
well sampled: shouldn't they agree?
22ns:
Cosine content  PC1 0.956255
Cosine content  PC2 0.00428106
Cosine content  PC3 0.000162083

1st 11ns:
Cosine content  PC1 0.923261
Cosine content  PC2  0.0217681
Cosine content  PC3 0.0135543

2nd 11ns:
Cosine content  PC1 0.786694
Cosine content  PC2 0.1654
Cosine content  PC3 0.000335589

Are we doing something wrong? Is this the exptected behaviour?
This is what we do to calculate the PCA's (10ns of equilibration removed):
g_covar -f trajectory.xtc -b 1 -e 21000 -s structure.pdb -o
eigenval-T300-A.xvg -v eigenvec-T300-A.trr -av average-pca-T300-A.pdb
g_covar -f trajectory.xtc -b 21020 -s structure.pdb -o
eigenval-T300-B.xvg -v eigenvec-T300-B.trr -av average-pca-T300-B.pdb

and to compare them:
g_anaeig -inpr T300-A-B.xpm -v eigenvec-T300-A.trr -v2
eigenvec-T300-B.trr -first 1 -last 10

Thanks for your help and suggestions!
Ramon
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Re: [gmx-users] monomer's conectivity

2008-10-23 Thread Andrea Muntean 
Thank you. I hope this helps me further.
My system is 32 polystyrene chains of 80 monomers.
Andrea
2008/10/23 Mark Abraham <[EMAIL PROTECTED]>

> Andrea Muntean wrote:
>
>> Thank you for your answer.
>>  If I am looking at the PDB standard format and my file, I observe that I
>> have only one number between the type of residue and coordinates, and I
>> suppose it is the residue current number. I am indeed missing the chain
>> identifier code, which should be of A1 Fortran format, which I don't really
>> understand (one carachter, but I have 32 chains, so it should be minimum A2
>> or I2). That I could introduce.
>>
>
> Get a PDB file with just one polymer molecule and work on getting a
> topology for that. Walking before running :-)
>
> In my pdb entries I dont define any connectors. Should they be a dummy
>> atom, with the corresponding bond, angle, dihedhral, which after that I
>> redefine in the tdb file?
>>
>
> First you need a functional *residue topology*. Check chapter 5 of the
> manual and look at the other force fields to see how (for example) protein
> force fields define the connectors with + and - prefixes. Once you've got
> that, then it's possible for pdb2gmx to join them head to tail (using the
> residue number field to indicate the breaks, and the name to match up with
> the topology you've defined), and you may then need either terminating
> residues of a different name or a .tdb entry.
>
> I dont think it is a visualisation artefact, because it really gives less
>> number of bonds, corresponding to the missing intermonomeric bonds.
>>
>
> Your visualization software is not reading a file format that is encoding
> any topology (since you haven't produced one yet). Thus it's inventing some
> bonds based on the coordinates. The output of pdb2gmx that contains topology
> information is the .top file, not the coordinate file.
>
> Should I do now both (introducing a chain identifier in the pdb, but how?,
>> and defining the intermonomeric bonds via dummy in the pdb and tdb?)?
>>
>
> I suppose there are some circumstances where chain identifiers might be
> useful, but since you haven't even told us what your monomer and system are,
> it's hard to help you.
>
>
> Mark
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Re: [gmx-users] monomer's conectivity

2008-10-23 Thread Mark Abraham 

Andrea Muntean wrote:

Thank you for your answer.
 
If I am looking at the PDB standard format and my file, I observe that I 
have only one number between the type of residue and coordinates, and I 
suppose it is the residue current number. I am indeed missing the chain 
identifier code, which should be of A1 Fortran format, which I don't 
really understand (one carachter, but I have 32 chains, so it should be 
minimum A2 or I2). That I could introduce.


Get a PDB file with just one polymer molecule and work on getting a 
topology for that. Walking before running :-)


In my pdb entries I dont define any connectors. Should they be a dummy 
atom, with the corresponding bond, angle, dihedhral, which after that I 
redefine in the tdb file?


First you need a functional *residue topology*. Check chapter 5 of the 
manual and look at the other force fields to see how (for example) 
protein force fields define the connectors with + and - prefixes. Once 
you've got that, then it's possible for pdb2gmx to join them head to 
tail (using the residue number field to indicate the breaks, and the 
name to match up with the topology you've defined), and you may then 
need either terminating residues of a different name or a .tdb entry.


I dont think it is a visualisation artefact, because it really gives 
less number of bonds, corresponding to the missing intermonomeric bonds.


Your visualization software is not reading a file format that is 
encoding any topology (since you haven't produced one yet). Thus it's 
inventing some bonds based on the coordinates. The output of pdb2gmx 
that contains topology information is the .top file, not the coordinate 
file.


Should I do now both (introducing a chain identifier in the pdb, but 
how?, and defining the intermonomeric bonds via dummy in the pdb and tdb?)?


I suppose there are some circumstances where chain identifiers might be 
useful, but since you haven't even told us what your monomer and system 
are, it's hard to help you.


Mark
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Re: [gmx-users] g_rotacf

2008-10-23 Thread Stephanus Fengler 

Daniel K wrote:

How should I change it so it calculates the 40 ps?

You need at least a 80ps trajectory otherwise you basically have too 
less  data to correlate with with a lag time of 40ps.

Check gromacs manual 4.0 at section 8.5
On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole <[EMAIL PROTECTED] 
> wrote:


On Wed, 22 Oct 2008 17:38:58 -0400
 "Daniel K" <[EMAIL PROTECTED] > wrote:

I have been trying to use g_rotacf with a simulation run for
40 ps (2)
with steps of 2fs and the frames where extracted every 50 fs
(25 frames).
The trajectory file is correct because it has 801 frames. When
I calculate
the g_rotacf I only get 20 ps and the time step is 50 fs. Does
any body no
why?

What is wrong with this? By default g_rotacf plots only half of
the time
correlation function ...
I do not know what you looking at but 40 ps is pretty short
simulation.

 


This is the header and end of the file that I get
# This file was created Mon Oct 20 11:38:06 2008
# by the following command:
# g_rotacf -P 2 -f md_noT.trr -s md_noT.tpr -n NC.ndx -o
md_noT_ACF.xvg -d
#
# g_rotacf is part of G R O M A C S:
#
# Glycine aRginine prOline Methionine Alanine Cystine Serine
#
@title "Rotational Correlation Function"
@xaxis  label "Time (ps)"
@yaxis  label "C(t)"
@TYPE xy
   0.000 1.0
   0.050 0.95376
   0.100 0.90907
 
  19.800-0.22896
  19.850-0.22921
  19.900-0.23028
  19.950-0.23078
  20.000-0.23111
&


-
XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands
-
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Re: [gmx-users] Is there force field for the heavy ions?

2008-10-23 Thread Mark Abraham 

G.H. Zuo wrote:

Dear Gromacs users

I want do some studies about the As and Sn. But I can't found them in 
the regular force field, including
oplsaa and amber.  How can I get the parameters for these ions? Or there 
are some method to obtain

these parameters?


... with difficulty. See 
http://wiki.gromacs.org/index.php/Exotic_Species in the first instance.


Mark
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RE: [gmx-users] Smallest allowed cell size

2008-10-23 Thread Berk Hess 
Hi,

This sounds like the pgi compiler bug which has been reported before,
although maybe not on one of the gmx lists.
I assume you are compiling with a somewhat older version of pgi.
Update to the newest version of pgi or use gcc.

Berk


> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Date: Wed, 22 Oct 2008 16:52:59 -0700
> Subject: [gmx-users] Smallest allowed cell size
> 
> Hi,
> 
> I received the following error
> 
> ---
> Program mdrun, VERSION 4.0
> Source code file: domdec.c, line: 2933
> 
> Fatal error:
> Step 10: The X-size (-32.295326) times the triclinic skew factor (1.00)
> is smaller than the smallest allowed cell size (1.20) for domain
> decomposition grid cell 0 0 0
> ---
> 
> under the following conditions
> 
> GROMACS 4.0 installed on a Cray XT4 at nics.utk.edu
> 
> #PBS -l walltime=12:00:00,size=16
> aprun -n 16 mdrun -maxh 29.5
> 
> The system has 84272 atoms in a box that is approx. 10x10x10. It works with
> 8 processors but I would think that this is fine divided up between 16
> processors.
> 
> Any suggestions for understanding this error message would be appreciated.
> 
> Thanks,
> Matt
> 
> -
> Matthew Hoopes
> Biophysics Graduate Group
> University of California, Davis
> 
> [EMAIL PROTECTED]
> 530-752-6452
> - 
> 
> 
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[gmx-users] Is there force field for the heavy ions?

2008-10-23 Thread G.H. Zuo 
Dear Gromacs users

I want do some studies about the As and Sn. But I can't found them in the
regular force field, including
oplsaa and amber.  How can I get the parameters for these ions? Or there are
some method to obtain
these parameters?

Thanks!

G.H.Zuo
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Re: [gmx-users] monomer's conectivity

2008-10-23 Thread Andrea Muntean 
Thank you for your answer.

If I am looking at the PDB standard format and my file, I observe that I
have only one number between the type of residue and coordinates, and I
suppose it is the residue current number. I am indeed missing the chain
identifier code, which should be of A1 Fortran format, which I don't really
understand (one carachter, but I have 32 chains, so it should be minimum A2
or I2). That I could introduce.
In my pdb entries I dont define any connectors. Should they be a dummy atom,
with the corresponding bond, angle, dihedhral, which after that I redefine
in the tdb file?
I dont think it is a visualisation artefact, because it really gives less
number of bonds, corresponding to the missing intermonomeric bonds.

Should I do now both (introducing a chain identifier in the pdb, but how?,
and defining the intermonomeric bonds via dummy in the pdb and tdb?)?

Thanks again for your help.

Best regards,
Andrea
2008/10/22 Mark Abraham <[EMAIL PROTECTED]>

>  Andrea Muntean wrote:
>
>> I have a *pdb file for a polymer box which I want to use. I defined the
>> residues (the first, the last and the inner monomers).
>> Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M
>> monomers each.
>> My problem now is how to connect the monomers. What is the best way to do
>> so?
>>
>
> We can't tell yet. You might have a PDB file with each residue in its own
> chain. You might have defined residue topologies without suitable
> connectors. You might be observing a visualization artefact. You might have
> some warnings from pdb2gmx you haven't observed yet.
>
> Mark
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