Re: [gmx-users] Normal Mode Analysis

[James Starlight]

As the consequence I've done my NMA calculations without of any constraints
:)

integrator= nm; Normal Mode Analysis
constraints =  none


but I'm not sure if this could be valid because I didnt found any literature
of such NMA in Gromacs. Could someone provide me with the appropriate
cut-offs for the NMA in gromacs?

By the way before this NMA I've done 2 energy minimization calculations
first by Steepest algorithm (emtool= 1000) and then by CG ( emtool=10)
but resulting force was still not small enought (8.92766e+02). How I can
futher minimize my structurere?

Finally I've forced with the diffuculty of the analysing of my data by the
g_anaeig
E,g I want to obtain fluctuations of some atoms from my eigenvectors
g_anaeig -s fornma22.tpr -v eigenvec.trr -eig eigenval2.xvg -rmsf -first -1
1 0

I've obtained a .xvg file fith the fluctuations along 1st mode but during
opening that file by xgrace I've obtain some input error. Whats I've done
wrong ?


Thanks,
James


2011/10/23 James Starlight 

> I want to come back to the question of the NMA in the Gromacs :)
>
> I've found in manual possible algorithms of this analysis-  I must
> calculate Hessian matrix via Md-run and then calculate modes with g_nmens
> program
>
>
> 1- I've performed CG minimization of my initianl structure
>
> 2- I've loadet to the gromp .tpr file of my minimized structure
>
> 3-  I've used mdrun and obtain error
> Fatal error:
> Constraints present with Normal Mode Analysis, this combination is not
> supported
>
> So I suppose that the problem with my .mdp file wich consist of the
> parametres for the NMA of Lyzosyme in water :)
>
> integrator= nm; Normal Mode Analysis
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist= 1; Frequency to update the neighbor list and long
> range forces
> ns_type= grid; Method to determine neighbor list (simple,
> grid)
> rlist= 1.0; Cut-off for making neighbor list (short range
> forces)
> coulombtype= PME; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.0; Short-range electrostatic cut-off
> rvdw= 1.0; Short-range Van der Waals cut-off
> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>
>
> How I should edit this configure file for my NMA?
> If I edit the above parametries for rvdw etc in accardance to the
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nmI've
>  obtained error that
>
> ERROR 1 [file nma.mdp]:
>   With coulombtype = PME, rcoulomb must be equal to rlist
>   If you want optimal energy conservation or exact integration use
> PME-Switch
>
>
> ERROR 2 [file nma.mdp]:
>   With vdwtype = Cut-off, rvdw must be >= rlist
>
> What are the most suitable coulombtype for the NMA and combination of the
> other options?
>
>
> James
>
>
>
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[gmx-users] ATP+Mg

[Алексей Раевский]

Hi all. I need your advices about my task which is closely associated with
ATP toplogy in the binding site. As I understood from one of the letters (
http://archive.ambermd.org/201106/0522.html) I can use antechamber or derive
charges from the site linked in the letter. But the ATP's phosphate tail is
very flexible and very negatevly charged thus I need too coordinate it with
Mg ion to prevent an increased flexibility and motion. Here are some of my
questions:
1. What parts of initial structure I have to prepare and process with
antechamber - separate adenylate and metal or both of them together like a
compound?
2. After getting separate topologys / complex topology - is it necessary to
constrain the distances between PO2 groups and metal to be sure this tail
won't move anyway during MD or this coordination bond is strong enough?

Thank you

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*

Nemo me impune lacessit*
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 24/10/2011 3:12 AM, James Starlight wrote:

I want to come back to the question of the NMA in the Gromacs :)

I've found in manual possible algorithms of this analysis-  I must 
calculate Hessian matrix via Md-run and then calculate modes with 
g_nmens program



1- I've performed CG minimization of my initianl structure

2- I've loadet to the gromp .tpr file of my minimized structure

3-  I've used mdrun and obtain error
Fatal error:
Constraints present with Normal Mode Analysis, this combination is not 
supported


So I suppose that the problem with my .mdp file wich consist of the 
parametres for the NMA of Lyzosyme in water :)


integrator= nm; Normal Mode Analysis

; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions
nstlist= 1; Frequency to update the neighbor list and 
long range forces
ns_type= grid; Method to determine neighbor list 
(simple, grid)
rlist= 1.0; Cut-off for making neighbor list (short 
range forces)
coulombtype= PME; Treatment of long range electrostatic 
interactions

rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)


How I should edit this configure file for my NMA?
If I edit the above parametries for rvdw etc in accardance to the 
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nm 
I've obtained error that


ERROR 1 [file nma.mdp]:
  With coulombtype = PME, rcoulomb must be equal to rlist
  If you want optimal energy conservation or exact integration use 
PME-Switch



ERROR 2 [file nma.mdp]:
  With vdwtype = Cut-off, rvdw must be >= rlist

What are the most suitable coulombtype for the NMA and combination of 
the other options?


That .mdp file did not produce that output.

Mark
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 24/10/2011 6:56 PM, James Starlight wrote:
As the consequence I've done my NMA calculations without of any 
constraints :)


integrator= nm; Normal Mode Analysis
constraints =  none


but I'm not sure if this could be valid because I didnt found any 
literature of such NMA in Gromacs. Could someone provide me with the 
appropriate cut-offs for the NMA in gromacs?


These are particular to the force field involved, not the software. 
Please consult the appropriate literature, and see what others have used 
for similar work.




By the way before this NMA I've done 2 energy minimization calculations
first by Steepest algorithm (emtool= 1000) and then by CG ( emtool=10)
but resulting force was still not small enought (8.92766e+02). How I 
can futher minimize my structurere?


Smaller EM steps might do something.



Finally I've forced with the diffuculty of the analysing of my data by 
the  g_anaeig

E,g I want to obtain fluctuations of some atoms from my eigenvectors
g_anaeig -s fornma22.tpr -v eigenvec.trr -eig eigenval2.xvg -rmsf 
-first -1

1 0

I've obtained a .xvg file fith the fluctuations along 1st mode but 
during opening that file by xgrace I've obtain some input error. Whats 
I've done wrong ?


We can't tell from this information.

Mark




Thanks,
James


2011/10/23 James Starlight >


I want to come back to the question of the NMA in the Gromacs :)

I've found in manual possible algorithms of this analysis-  I must
calculate Hessian matrix via Md-run and then calculate modes with
g_nmens program


1- I've performed CG minimization of my initianl structure

2- I've loadet to the gromp .tpr file of my minimized structure

3-  I've used mdrun and obtain error
Fatal error:
Constraints present with Normal Mode Analysis, this combination is
not supported

So I suppose that the problem with my .mdp file wich consist of
the parametres for the NMA of Lyzosyme in water :)

integrator= nm; Normal Mode Analysis

; Parameters describing how to find the neighbors of each atom and
how to calculate the interactions
nstlist= 1; Frequency to update the neighbor list
and long range forces
ns_type= grid; Method to determine neighbor list
(simple, grid)
rlist= 1.0; Cut-off for making neighbor list
(short range forces)
coulombtype= PME; Treatment of long range
electrostatic interactions
rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)


How I should edit this configure file for my NMA?
If I edit the above parametries for rvdw etc in accardance to the

http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nm
I've obtained error that

ERROR 1 [file nma.mdp]:
  With coulombtype = PME, rcoulomb must be equal to rlist
  If you want optimal energy conservation or exact integration use
PME-Switch


ERROR 2 [file nma.mdp]:
  With vdwtype = Cut-off, rvdw must be >= rlist

What are the most suitable coulombtype for the NMA and combination
of the other options?


James







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[gmx-users] trjconv - PBC

[Steven Neumann]

Dear Gmx Users,

I am trying to convert my trajectory using trjconv.  My system is made of 10
ligands and protein. Protein is jumping
divided into parts. The same is with my ligands. I am confused about the
point 2 and 3:



2. Extract the first frame from the trajectory as reference for removing
jumps if you want to remove jumps.



Which option of trjconv is responsible for extraction of my 1st frame?



3. Remove jumps if you want to have them removed using the first frame



trjconv -f traj.xtc -s *.tpr -pbc nojump (how to use 1st frame here
extracted from previous point?)





I would be really thankful!



Steven
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Re: [gmx-users] trjconv - PBC

[Justin A. Lemkul]

Steven Neumann wrote:

Dear Gmx Users,
 
I am trying to convert my trajectory using trjconv.  My system is made 
of 10 ligands and protein. Protein is jumping 
divided into parts. The same is with my ligands. I am confused about the 
point 2 and 3:
 
 

2. Extract the first frame from the trajectory as reference for removing 
jumps if you want to remove jumps.


 


Which option of trjconv is responsible for extraction of my 1st frame?

 


trjconv -dump 0



3. Remove jumps if you want to have them removed using the first frame

 

trjconv -f traj.xtc -s *.tpr -pbc nojump (how to use 1st frame here 
extracted from previous point?)


 


Recreate the .tpr file using the coordinate file produced in (2).

-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] trjconv - PBC

[Tsjerk Wassenaar]

Hi,

You don't need a .tpr file for removing jumps; a pdb/gro file will do.

Cheers,

Tsjerk

On Oct 24, 2011 2:51 PM, "Justin A. Lemkul"  wrote:

Steven Neumann wrote: > > Dear Gmx Users, >  I am trying to convert my
trajectory using trjconv.  ...
trjconv -dump 0

> > 3. Remove jumps if you want to have them removed using the first frame >
>   > trjconv -f traj...
Recreate the .tpr file using the coordinate file produced in (2).

-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] trjconv - PBC

[Steven Neumann]

Sorry guys but I do not get this...


I used:

1. First make your molecules whole if you want them whole


trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc  (I have chosen my
whole system for input and output)



2. I do not need cluster anything

3. Extract the first frame from the trajectory as reference for removing
jumps if you want to remove jumps.



trjconv -f md2whole.xtc -s md2.tpr -dump 0 -o md2wholeDUMP.xtc   ???



I did not obtain any coordinate file as output can be only trajectory (trr
or xtc file)



4. How to use this frame in:



trjconv -f md2wholeDUMP.xtc -s md2.tpr -pbc nojump -o md2wholeDUMPnojump.xtc
?



Please, help!



Steven






On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar  wrote:

> Hi,
>
> You don't need a .tpr file for removing jumps; a pdb/gro file will do.
>
> Cheers,
>
> Tsjerk
>
> On Oct 24, 2011 2:51 PM, "Justin A. Lemkul"  wrote:
>
> Steven Neumann wrote: > > Dear Gmx Users, >  I am trying to convert my
> trajectory using trjconv.  ...
> trjconv -dump 0
>
> > > 3. Remove jumps if you want to have them removed using the first frame
> > >   > trjconv -f traj...
> Recreate the .tpr file using the coordinate file produced in (2).
>
> -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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> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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>
>
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Re: [gmx-users] trjconv - PBC

[Tsjerk Wassenaar]

Hi Steven,

Output can also be .pdb or .gro

Cheers,

Tsjerk

On Oct 24, 2011 3:59 PM, "Steven Neumann"  wrote:

Sorry guys but I do not get this...


I used:

1. First make your molecules whole if you want them whole


trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc  (I have chosen my
whole system for input and output)



2. I do not need cluster anything

3. Extract the first frame from the trajectory as reference for removing
jumps if you want to remove jumps.



trjconv -f md2whole.xtc -s md2.tpr -dump 0 -o md2wholeDUMP.xtc   ???



I did not obtain any coordinate file as output can be only trajectory (trr
or xtc file)



4. How to use this frame in:



trjconv -f md2wholeDUMP.xtc -s md2.tpr -pbc nojump -o md2wholeDUMPnojump.xtc
?



Please, help!



Steven






On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar  wrote:
> > Hi, > > You don't n...

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Re: [gmx-users] trjconv - PBC

[Steven Neumann]

Thank you both!!!

Steven

On Mon, Oct 24, 2011 at 3:01 PM, Tsjerk Wassenaar  wrote:

> Hi Steven,
>
> Output can also be .pdb or .gro
>
> Cheers,
>
> Tsjerk
>
>  On Oct 24, 2011 3:59 PM, "Steven Neumann"  wrote:
>
> Sorry guys but I do not get this...
>
>
> I used:
>
> 1. First make your molecules whole if you want them whole
>
>
> trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc  (I have chosen
> my whole system for input and output)
>
>
>
> 2. I do not need cluster anything
>
> 3. Extract the first frame from the trajectory as reference for removing
> jumps if you want to remove jumps.
>
>
>
> trjconv -f md2whole.xtc -s md2.tpr -dump 0 -o md2wholeDUMP.xtc   ???
>
>
>
> I did not obtain any coordinate file as output can be only trajectory (trr
> or xtc file)
>
>
>
> 4. How to use this frame in:
>
>
>
> trjconv -f md2wholeDUMP.xtc -s md2.tpr -pbc nojump -o
> md2wholeDUMPnojump.xtc ?
>
>
>
> Please, help!
>
>
>
> Steven
>
>
>
>
>
>
> On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar 
> wrote: > > Hi, > > You don't n...
>
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[gmx-users] failure during compiling gromacs 4.5.5

[Ye MEI]

Dear Gromacs users,

I am trying to install gromacs on my cluster using Intel Compiler 11.1.072 and 
FFTW3. But I met the following error message
 icc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 
-I../../../include -I/usr/local/include -xHOST 
-I/home/users/ymei/software/fftw3/intel/include -pthread -I./include -MT 
type.lo -MD -MP -MF .deps/type.Tpo -c type.c -o type.o
/tmp/iccLPSVQqas_.s: Assembler messages:
/tmp/iccLPSVQqas_.s:92: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:100: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
/tmp/iccLPSVQqas_.s:228: Error: no such instruction: `pminsb %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:236: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
/tmp/iccLPSVQqas_.s:2559: Error: no such instruction: `pmaxsd %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:2567: Error: no such instruction: `pmaxsd 
(%rdx,%r9,4),%xmm0'
/tmp/iccLPSVQqas_.s:2709: Error: no such instruction: `pminsd %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:2717: Error: no such instruction: `pminsd 
(%rdx,%r9,4),%xmm0'
/tmp/iccLPSVQqas_.s:2989: Error: no such instruction: `pmulld %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:2997: Error: no such instruction: `pmulld 
(%rdx,%rax,4),%xmm0'
/tmp/iccLPSVQqas_.s:7009: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:7017: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
/tmp/iccLPSVQqas_.s:7145: Error: no such instruction: `pminsb %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:7153: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
/tmp/iccLPSVQqas_.s:9313: Error: no such instruction: `pmaxuw %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:9321: Error: no such instruction: `pmaxuw 
(%rdx,%r9,2),%xmm0'
/tmp/iccLPSVQqas_.s:9463: Error: no such instruction: `pminuw %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:9471: Error: no such instruction: `pminuw 
(%rdx,%r9,2),%xmm0'
/tmp/iccLPSVQqas_.s:10621: Error: no such instruction: `pmaxud %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:10629: Error: no such instruction: `pmaxud 
(%rdx,%r9,4),%xmm0'
/tmp/iccLPSVQqas_.s:10771: Error: no such instruction: `pminud %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:10779: Error: no such instruction: `pminud 
(%rdx,%r9,4),%xmm0'
/tmp/iccLPSVQqas_.s:11051: Error: no such instruction: `pmulld %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:11059: Error: no such instruction: `pmulld 
(%rdx,%rax,4),%xmm0'
/tmp/iccLPSVQqas_.s:15514: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:15522: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
/tmp/iccLPSVQqas_.s:15650: Error: no such instruction: `pminsb %xmm0,%xmm1'
/tmp/iccLPSVQqas_.s:15658: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
make[4]: *** [type.lo] Error 1
make[4]: Leaving directory 
`/home/users/ymei/software/gromacs-4.5.5/src/gmxlib/thread_mpi'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src/gmxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src'
make: *** [all-recursive] Error 1

I have never seen this kind of error message before, and I donot know what to 
do to solve this problem. Can anyone help me out?
Intel Compiler 2011 is ok. But this version does not work well with my cluster, 
especially with openmpi.

And the following information might be helpful.

ymei@CLOUD@ECNU:~/software/gromacs-4.5.5> gcc -v
Using built-in specs.
Target: x86_64-suse-linux
Configured with: ../configure --enable-threads=posix --prefix=/usr 
--with-local-prefix=/usr/local --infodir=/usr/share/info 
--mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 
--enable-languages=c,c++,objc,fortran,obj-c++,java,ada 
--enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 
--enable-ssp --disable-libssp --disable-libgcj --with-slibdir=/lib64 
--with-system-zlib --enable-shared --enable-__cxa_atexit 
--enable-libstdcxx-allocator=new --program-suffix= 
--enable-version-specific-runtime-libs --without-system-libunwind 
--with-cpu=generic --host=x86_64-suse-linux
Thread model: posix
gcc version 4.1.2 20070115 (SUSE Linux)

ymei@CLOUD@ECNU:~/software/gromacs-4.5.5> cat /etc/SuSE-release
SUSE Linux Enterprise Server 10 (x86_64)
VERSION = 10
PATCHLEVEL = 2

Thank you in advance.

Ye 
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[gmx-users] modeling cation-pi box

[EGY]

I am interesting in modeling a small molecule ligand-protein complex that 
involves a cationic ligand encapsulated by several aromatic residues that form 
a box around the cation. However, md simulations result in the cation moving 
outside the box. I am using the CHARMM27 forcefield. Is there a way to restrain 
the cation portion of the small molecule to within the aromatic box? Or is 
there a better forcefield, which will take these interactions into 
consideration.
Thanks.
Egy--
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Re: [gmx-users] trjconv - PBC

[Steven Neumann]

Last question:

I would like to visualise my whole trjajectory looking at one of the ligands
only which stacked to the loop of my protein. Which option of trjconv will
be suitable to see whole trajectory of this ligand withoout any shifts on
the screen so I will be able to produce a movie? I assume I need to use ndx
file of this ligand.

thank you in advance

Steven

On Mon, Oct 24, 2011 at 3:26 PM, Steven Neumann wrote:

> Thank you both!!!
>
> Steven
>
>   On Mon, Oct 24, 2011 at 3:01 PM, Tsjerk Wassenaar wrote:
>
>> Hi Steven,
>>
>> Output can also be .pdb or .gro
>>
>> Cheers,
>>
>> Tsjerk
>>
>>  On Oct 24, 2011 3:59 PM, "Steven Neumann"  wrote:
>>
>> Sorry guys but I do not get this...
>>
>>
>> I used:
>>
>> 1. First make your molecules whole if you want them whole
>>
>>
>> trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc  (I have chosen
>> my whole system for input and output)
>>
>>
>>
>> 2. I do not need cluster anything
>>
>> 3. Extract the first frame from the trajectory as reference for removing
>> jumps if you want to remove jumps.
>>
>>
>>
>> trjconv -f md2whole.xtc -s md2.tpr -dump 0 -o md2wholeDUMP.xtc   ???
>>
>>
>>
>> I did not obtain any coordinate file as output can be only trajectory (trr
>> or xtc file)
>>
>>
>>
>> 4. How to use this frame in:
>>
>>
>>
>> trjconv -f md2wholeDUMP.xtc -s md2.tpr -pbc nojump -o
>> md2wholeDUMPnojump.xtc ?
>>
>>
>>
>> Please, help!
>>
>>
>>
>> Steven
>>
>>
>>
>>
>>
>>
>> On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar 
>> wrote: > > Hi, > > You don't n...
>>
>> --
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>>
>>
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>>
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Re: [gmx-users] modeling cation-pi box

[Justin A. Lemkul]

EGY wrote:

I am interesting in modeling a small molecule ligand-protein complex that 
involves a cationic ligand encapsulated by several aromatic residues that form 
a box around the cation. However, md simulations result in the cation moving 
outside the box. I am using the CHARMM27 forcefield. Is there a way to restrain 
the cation portion of the small molecule to within the aromatic box? Or is 
there a better forcefield, which will take these interactions into 
consideration.


More than likely you simply need to account for periodicity.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin


Thanks.
Egy-- 
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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] trjconv - PBC

[Justin A. Lemkul]

Steven Neumann wrote:

Last question:
 
I would like to visualise my whole trjajectory looking at one of the 
ligands only which stacked to the loop of my protein. Which option of 
trjconv will be suitable to see whole trajectory of this ligand withoout 
any shifts on the screen so I will be able to produce a movie? I assume 
I need to use ndx file of this ligand.
 


trjconv -center

Select the ligand as the group to be centered.  This approach may not work well 
if there are large changes in position over time, so I'm guessing a bit. 
Otherwise trjconv -fit may work, or centering on some suitable group with which 
the ligand interacts.


-Justin


thank you in advance
 
Steven


On Mon, Oct 24, 2011 at 3:26 PM, Steven Neumann > wrote:


Thank you both!!!
 
Steven


On Mon, Oct 24, 2011 at 3:01 PM, Tsjerk Wassenaar mailto:tsje...@gmail.com>> wrote:

Hi Steven,

Output can also be .pdb or .gro

Cheers,

Tsjerk


On Oct 24, 2011 3:59 PM, "Steven Neumann"
mailto:s.neuman...@gmail.com>> wrote:

Sorry guys but I do not get this...
 
 
I used:
 
1. First make your molecules whole if you want them whole
 


trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc  (I
have chosen my whole system for input and output)

 


2. I do not need cluster anything

3. Extract the first frame from the trajectory as reference
for removing jumps if you want to remove jumps.

 


trjconv -f md2whole.xtc -s md2.tpr -dump 0 -o
md2wholeDUMP.xtc   ???

 


I did not obtain any coordinate file as output can be only
trajectory (trr or xtc file)

 


4. How to use this frame in:

 


trjconv -f md2wholeDUMP.xtc -s md2.tpr -pbc nojump -o
md2wholeDUMPnojump.xtc ?

 


Please, help!

 


Steven

 

 




On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar
mailto:tsje...@gmail.com>> wrote: > > Hi,
> > You don't n...


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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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[gmx-users] Lyzosyme with ligand tutorial

[James Starlight]

Justin, hello!


I have forced with some problem during final stage of your turorial.

I dont know why but after NPT phase my sytem has occured in the standart
cubic box instead of dodecahedron (after all previosly phases my system was
in correct box).

So when I've passed my system in the MD stage- it's moved back into normal
dodecahedron box but on the placement where previously system was. So as the
consequence I've obtained protein in the wrong place ( some of its parts
were outside new box )

I've tried examined why this might occur but have not found possible
explanations.

I've examined box coordinates of the all .gro structurs obtained after each
of the stages and all of them contained such box vectors
7.85059   7.85059   5.55120   0.0   0.0   0.0   0.0
3.92529   3.92529

As I understood It's correspond to the system in the dodecahedron box but my
ntp.gro structure with the same is in the cubic box ( with the above box
coordinates as well). Why its might occured and were else information of the
box coordinates is present exept of initial structure gro file ?


James
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

I understand this but I've not been able found such information. I dont need
in the most accurately  parametries for all cutt-offs of my system but I
want to gain inside into the basic cutt- offs worked with the Normal mode
analysis.

E.g I've found that PME is not worked here. So I must to constrain my system
with simplest cuttoffs. Could you provide me with the simple example e.g
cutt of for interaction beetwen C-alpha atoms only etc?

James



> These are particular to the force field involved, not the software. Please
> consult the appropriate literature, and see what others have used for
> similar work.
>
>
>
>
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Re: [gmx-users] modeling cation-pi box

[EGY]

Thanks for taking the time to answer, but I think my wording may have confused 
my question. I shouldn't have used the word box. Within the protein their are 
several aromatic residues that interact with the small molecule cation. I would 
like to preserve these interactions throughout the simulations. Is it possible 
to "enhance" these interactions, since there is no defined force constants that 
describes these interactions?
Thanks.
Egy


On Oct 24, 2011, at 12:19 PM, Justin A. Lemkul wrote:

> 
> 
> EGY wrote:
>> I am interesting in modeling a small molecule ligand-protein complex that 
>> involves a cationic ligand encapsulated by several aromatic residues that 
>> form a box around the cation. However, md simulations result in the cation 
>> moving outside the box. I am using the CHARMM27 forcefield. Is there a way 
>> to restrain the cation portion of the small molecule to within the aromatic 
>> box? Or is there a better forcefield, which will take these interactions 
>> into consideration.
> 
> More than likely you simply need to account for periodicity.
> 
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> 
> -Justin
> 
>> Thanks.
>> Egy-- 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] Lyzosyme with ligand tutorial

[Justin A. Lemkul]

James Starlight wrote:

Justin, hello!


I have forced with some problem during final stage of your turorial.

I dont know why but after NPT phase my sytem has occured in the standart 
cubic box instead of dodecahedron (after all previosly phases my system 
was in correct box).


So when I've passed my system in the MD stage- it's moved back into 
normal dodecahedron box but on the placement where previously system 
was. So as the consequence I've obtained protein in the wrong place ( 
some of its parts were outside new box )


I've tried examined why this might occur but have not found possible 
explanations.


I've examined box coordinates of the all .gro structurs obtained after 
each of the stages and all of them contained such box vectors
7.85059   7.85059   5.55120   0.0   0.0   0.0   0.0   
3.92529   3.92529


As I understood It's correspond to the system in the dodecahedron box 
but my ntp.gro structure with the same is in the cubic box ( with the 
above box coordinates as well). Why its might occured and were else 
information of the box coordinates is present exept of initial structure 
gro file ?




You still have a dodecahedral box.  The default representation is a simple 
triclinic cell.  A true compact representation can be obtained with:


trjconv -pbc mol -ur compact

-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] modeling cation-pi box

[Justin A. Lemkul]

EGY wrote:

Thanks for taking the time to answer, but I think my wording may have confused my 
question. I shouldn't have used the word box. Within the protein their are several 
aromatic residues that interact with the small molecule cation. I would like to preserve 
these interactions throughout the simulations. Is it possible to "enhance" 
these interactions, since there is no defined force constants that describes these 
interactions?


The only way to manually maintain these interactions is to use the pull code, 
which does require that some force constant be set.  The other option, of 
course, is to re-derive more suitable parameters.  If the system does not follow 
realistic behavior, then the model must be adjusted in some way.


-Justin


Thanks.
Egy


On Oct 24, 2011, at 12:19 PM, Justin A. Lemkul wrote:



EGY wrote:

I am interesting in modeling a small molecule ligand-protein complex that 
involves a cationic ligand encapsulated by several aromatic residues that form 
a box around the cation. However, md simulations result in the cation moving 
outside the box. I am using the CHARMM27 forcefield. Is there a way to restrain 
the cation portion of the small molecule to within the aromatic box? Or is 
there a better forcefield, which will take these interactions into 
consideration.

More than likely you simply need to account for periodicity.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin


Thanks.
Egy-- gmx-users mailing listgmx-users@gromacs.org
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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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--


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] Lyzosyme with ligand tutorial

[James Starlight]

Justin,

I've used trjconv -pbc mol -ur compact
but the final picture was still wrong :(

So I think that something happened with my box  because

1- If the cubic representation is set on default why other .gro structures
were visualized in VMD in dodecahedral box on default ?

2- Why the pereodic boundaries were distorded in the next stage after NPT
(production MD) that my structure were outside the box on half ? I want to
point that on MD stage the box were dodecahedral again like in the NVT and
other stages but my structure was in wrong position.


James

2011/10/24 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Justin, hello!
>>
>>
>> I have forced with some problem during final stage of your turorial.
>>
>> I dont know why but after NPT phase my sytem has occured in the standart
>> cubic box instead of dodecahedron (after all previosly phases my system was
>> in correct box).
>>
>> So when I've passed my system in the MD stage- it's moved back into normal
>> dodecahedron box but on the placement where previously system was. So as the
>> consequence I've obtained protein in the wrong place ( some of its parts
>> were outside new box )
>>
>> I've tried examined why this might occur but have not found possible
>> explanations.
>>
>> I've examined box coordinates of the all .gro structurs obtained after
>> each of the stages and all of them contained such box vectors
>> 7.85059   7.85059   5.55120   0.0   0.0   0.0   0.0
>> 3.92529   3.92529
>>
>> As I understood It's correspond to the system in the dodecahedron box but
>> my ntp.gro structure with the same is in the cubic box ( with the above box
>> coordinates as well). Why its might occured and were else information of the
>> box coordinates is present exept of initial structure gro file ?
>>
>>
> You still have a dodecahedral box.  The default representation is a simple
> triclinic cell.  A true compact representation can be obtained with:
>
> trjconv -pbc mol -ur compact
>
> -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
>
> ==**==
> --
> 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/Searchbefore
>  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 
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Re: [gmx-users] failure during compiling gromacs 4.5.5

[Szilárd Páll]

Hi,

The error messages are all referring to SSE 4.1 packed integer min/max
operations not being recognized. I assume that these were enabled by
the "-xHOST" compiler option, and icc automatically generated these
instructions - the files it's complaining about are even temporary
files.

Could it be that you have a broken installation of Intel Compilers on
your cluster? You could check if it works if you remove -xHOST or
explicitly state -xSSE4.1.

Just for curiosity, what are the issues with the Intel Compiler 2011
(I assume that's 12.x) + OpenMPI?

Cheers,
--
Szilárd



On Mon, Oct 24, 2011 at 4:53 PM, Ye MEI  wrote:
> Dear Gromacs users,
>
> I am trying to install gromacs on my cluster using Intel Compiler 11.1.072
> and FFTW3. But I met the following error message
>  icc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 -I../../../include -I/usr/local/include -xHOST -I/home/users/ymei/software/fftw3/intel/include -pthread -I./include -MT type.lo -MD -MP -MF .deps/type.Tpo -c type.c -o type.o
> /tmp/iccLPSVQqas_.s: Assembler messages:
> /tmp/iccLPSVQqas_.s:92: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:100: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:228: Error: no such instruction: `pminsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:236: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:2559: Error: no such instruction: `pmaxsd %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:2567: Error: no such instruction: `pmaxsd (%rdx,%r9,4),%xmm0'
> /tmp/iccLPSVQqas_.s:2709: Error: no such instruction: `pminsd %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:2717: Error: no such instruction: `pminsd (%rdx,%r9,4),%xmm0'
> /tmp/iccLPSVQqas_.s:2989: Error: no such instruction: `pmulld %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:2997: Error: no such instruction: `pmulld (%rdx,%rax,4),%xmm0'
> /tmp/iccLPSVQqas_.s:7009: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:7017: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:7145: Error: no such instruction: `pminsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:7153: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:9313: Error: no such instruction: `pmaxuw %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:9321: Error: no such instruction: `pmaxuw (%rdx,%r9,2),%xmm0'
> /tmp/iccLPSVQqas_.s:9463: Error: no such instruction: `pminuw %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:9471: Error: no such instruction: `pminuw (%rdx,%r9,2),%xmm0'
> /tmp/iccLPSVQqas_.s:10621: Error: no such instruction: `pmaxud %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:10629: Error: no such instruction: `pmaxud (%rdx,%r9,4),%xmm0'
> /tmp/iccLPSVQqas_.s:10771: Error: no such instruction: `pminud %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:10779: Error: no such instruction: `pminud (%rdx,%r9,4),%xmm0'
> /tmp/iccLPSVQqas_.s:11051: Error: no such instruction: `pmulld %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:11059: Error: no such instruction: `pmulld (%rdx,%rax,4),%xmm0'
> /tmp/iccLPSVQqas_.s:15514: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:15522: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:15650: Error: no such instruction: `pminsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:15658: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
> make[4]: *** [type.lo] Error 1
> make[4]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src/gmxlib/thread_mpi'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src/gmxlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src'
> make: *** [all-recursive] Error 1
>
> I have never seen this kind of error message before, and I donot know what
> to do to solve this problem. Can anyone help me out?
> Intel Compiler 2011 is ok. But this version does not work well with my
> cluster, especially with openmpi.
>
> And the following information might be helpful.
>
> ymei@CLOUD@ECNU:~/software/gromacs-4.5.5> gcc -v
> Using built-in specs.
> Target: x86_64-suse-linux
> Configured with: ../configure --enable-threads=posix --prefix=/usr --with-local-prefix=/usr/local --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,java,ada --enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 --enable-ssp --disable-libssp --disable-libgcj --with-slibdir=/lib64 --with-system-zlib --enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=new --program-suffix= --enable-version-specific-runtime-libs --without-system-libunwind --with-cpu=generic --host=x86_64-suse-linux
> Thread model: posix
> gcc version 4.1.2 20070115 (SUSE Linux)
>
> ymei@CLOUD@ECNU:~/software/gromacs-4.5.5> cat /etc/SuSE-release
> SUSE Linux Enterprise Server 10 (x86_64)
> VER

Re: [gmx-users] Gromacs-GPU with an Nvidia GeForce GTX 580 error?

[Szilárd Páll]

Hi Matt,

Yes, you should use the "force-device=yes" option, the patch which was
meant to update the list of compatible GPUs didn't make it for 4.5.5.

Cheers,
--
Szilárd



On Sun, Oct 23, 2011 at 10:24 PM, Matt Larson  wrote:
> I am having an error trying to use a compiled mdrun-gpu on my GPU setup here:
>
>
> Fatal error:
> The selected GPU (#0, GeForce GTX 580) is not supported by Gromacs!
> Most probably you have a low-end GPU which would not perform well, or
> new hardware that has not been tested with the current release. If you
> still want to try using the device, use the force-device=yes option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> 
>
>  From what I can tell, the GTX 580 should be supported as of this
> version of gromacs (4.5.5) - as it is listed in the supported cards.
> I have openmm and CUDA libraries installed.
>
> - Openmm passes the test with
> /usr/local/openmm/bin/TestReferenceHarmonicBondForce.
> - NVIDIA driver is NVIDIA-Linux-x86_64-270.41.19
> (devdriver_4.0_linux_64_270.41.19.run patched with the
> nvidia_kernel-3.0-rc1.patch to let it be installed on ubuntu 11.10).
> - the NVIDIA_GPU_Computing_SDK examples run.
>
>  I've also tried with the normal NVIDIA x86_64-280.13 driver, but same error.
>
>  From the gromacs GPU page
> (http://www.gromacs.org/Downloads/Installation_Instructions/GPUs) it
> is clear that the GTX 580 has been run with gromacs.
>
>  Should I use the "force-device" option to use GTX 580, or is there a
> reason that gromacs doesn't think it has support for this GTX 580
> card?
>
>  Thanks much,
>  Matt Larson
> --
> gmx-users mailing list    gmx-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
>
--
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Re: [gmx-users] Lyzosyme with ligand tutorial

[Justin A. Lemkul]

James Starlight wrote:

Justin,

I've used trjconv -pbc mol -ur compact 
but the final picture was still wrong :(


So I think that something happened with my box  because

1- If the cubic representation is set on default why other .gro 
structures were visualized in VMD in dodecahedral box on default ?




VMD always defaults to a triclinic representation (since that is what is stored 
in Gromacs by default) unless the PBC is wrapped with -pbc mol -ur compact.  If 
VMD truly produces the pseudospherical shape, then trjconv was invoked somewhere 
along the way.


2- Why the pereodic boundaries were distorded in the next stage after 
NPT   (production MD) that my structure were outside the box on half ? I 
want to point that on MD stage the box were dodecahedral again like in 
the NVT and other stages but my structure was in wrong position.




I don't understand this statement.  You should also note that a periodic box has 
no "outside."  Perhaps it would be useful to post images online.  If you choose 
to do so, please follow bullet point #4 here:


http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette

-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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Please search the archive at 
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Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

[Szilárd Páll]

Please keep all discussions on the mailing list! Also, I'm also CC-ing
to the gmx-devel list, maybe somebody over there has an better what
causes your CMake issue.

>>> //Flags used by the compiler during all build types
>>> CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99  '
>>>
>>> //Flags used by the compiler during release builds.
>>> CMAKE_C_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2  -O3 -DNDEBUG
>>> ...
>>> These are obviously the wrong flags for the detected architecture,
>>> sse2 is no longer available and so are the the mtune architectures.
>>
>> Indeed, some of those flags are wrong (CXX -std=gnu99), others simply
>> outdated (-mtune=itanium2). There are plans to correct these issues
>> for 4.6, but let's agree on the fact that they are not show-stoppers
>> (FYI you won't get more than a few percent speedup with the right
>> compiler options, the most I've seen is ~5%.)
>
> OK, I was under the impression it would be simple to correct that -
> independend of gains if any.

Theoretically it is, but in practice not so much. Keeping up with the
ever changing compiler options - especially the architecture-related
optimization flags - is not a fun job. We'll try to improve these
aspects of the CMkake build system the next release.

>> If you want to get rid of them, the solution is pretty simple: just
>> remove the offending options and pick new ones if you think they work
>> better for you.
>
> That involves hand-editing the CMakeCache which may be no less
> bothersome than enduring the warnings ;-)

You can use ccmake (or cmake-gui), they will make your life easier.
Otherwise, editing the cache is nowhere near as difficult as it
sounds. ;)

>> However, I'm not sure what do you mean by "sse2 is no longer
>> available"? Of course it is, both the Intel Compiler and the majority
>> of current processors support it. Also, -mtune=core2 is perfectly
>> valid as is -msse2.
>
> I checked that with the documentation on the Intel site and
> the code generation options written out by the compiler (as
> help info). On the Intel site, -msse2 and -mtune=core2 are
> still listed as valid, whereas they aren't mentioned in the
> help provided by the compiler I installed. Maybe they are
> redundant with the Intel64-compiler and set by default
> (not entirely sure). Bottom line: you are right here, I
> missed some information.

i) Indded the "-msse2" is redundant. From the icc man page:

"On  Linux  systems, if neither -x nor -m is specified, the default is -msse2."

ii) Nope, the default as usually is -mtune=generic on "IA-32" and
"Intel 64" - as Intel likes to call them.

Btw, core2 is essentially equivalent with -xSSSE3. Depending on the
processors you intend to run on you can try -xSSE4.1 or -xSSE4.2, but
I doubt you'll see a noticeable difference.

>>> CMAKE_CXX_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99 '
>>
>> As Mark said, SSE3 won't help you in any noticeable way.
>
> The only 'help' I envisioned here was to avoid screen cluttering
> by loads of warnings. mMy suggested 'fixes' weren't really fixes,
> as I can see now. In my own development work, I can't stand
> pages of recurring warning messages ;-) So I probably
> overreacted here ...

Sure, warnings are not nice and we dislike them as well. That's why
these issues will be corrected in the future.

>>> But the install is broken. On `make install-mdrun`, the scripts would
>>> remove any library from "src/gmxlib/CMakeFiles/CMakeRelink.dir"
>>> and bail out with the error below. Even if you copy the libraries
>>> by hand to CMakeRelink.dir/, the'll get removed by make install-mdrun
>>> before trying to link with them.
>>
>> Now that is a bug. I'd appreciate if you could enter it in
>> redmine.gromacs.org withe all details on how to reproduce it!
>
> I didn't do that until now but examined this further. There is already
> an identical error posted by some other researcher (as you know):
> http://www.mail-archive.com/gmx-users@gromacs.org/msg39228.html
>
> I was able to replicate the error somehow on a different machine without
> any intel compiler around (when building with -DGMX_MPI=ON and cmake).
>
> Gromacs 4.5.5: autoconf/configure on SuSE 11.4/x64 on i7
> 
>                 icc/64-12.1.0    gcc/x64/4.5.1
> intThread           OK                OK
> MPI(1.3.2)          OK                OK
>
>
> Gromacs 4.5.5: cmake 2.8.3 on SuSE 11.4/x64 on i7
> 
>                 icc/64-12.1.0    gcc/x64/4.5.1
> intThread          error              OK
> MPI(1.3.2)         error             error
>
>
> Gromacs 4.5.5:  autoconf/configure on SuSE 11.4/x64 on Phenom/X4
> 
>                 gcc/x64/4.5.1    gcc/x64/4.6.1
> intThread           OK                OK
> MPI(1.3.2)          OK                OK
>
>
> Gromacs 4.5.5:  cmake 2.8.3 on SuSE 11.4/x6

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

[Szilárd Páll]

I've just realized that both you and the similar report you linked to
were using CMake 2.8.3. If you don't succeed could you try another
CMake version?
--
Szilárd



On Mon, Oct 24, 2011 at 11:14 PM, Szilárd Páll  wrote:
> Please keep all discussions on the mailing list! Also, I'm also CC-ing
> to the gmx-devel list, maybe somebody over there has an better what
> causes your CMake issue.
>
 //Flags used by the compiler during all build types
 CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99  '

 //Flags used by the compiler during release builds.
 CMAKE_C_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2  -O3 -DNDEBUG
 ...
 These are obviously the wrong flags for the detected architecture,
 sse2 is no longer available and so are the the mtune architectures.
>>>
>>> Indeed, some of those flags are wrong (CXX -std=gnu99), others simply
>>> outdated (-mtune=itanium2). There are plans to correct these issues
>>> for 4.6, but let's agree on the fact that they are not show-stoppers
>>> (FYI you won't get more than a few percent speedup with the right
>>> compiler options, the most I've seen is ~5%.)
>>
>> OK, I was under the impression it would be simple to correct that -
>> independend of gains if any.
>
> Theoretically it is, but in practice not so much. Keeping up with the
> ever changing compiler options - especially the architecture-related
> optimization flags - is not a fun job. We'll try to improve these
> aspects of the CMkake build system the next release.
>
>>> If you want to get rid of them, the solution is pretty simple: just
>>> remove the offending options and pick new ones if you think they work
>>> better for you.
>>
>> That involves hand-editing the CMakeCache which may be no less
>> bothersome than enduring the warnings ;-)
>
> You can use ccmake (or cmake-gui), they will make your life easier.
> Otherwise, editing the cache is nowhere near as difficult as it
> sounds. ;)
>
>>> However, I'm not sure what do you mean by "sse2 is no longer
>>> available"? Of course it is, both the Intel Compiler and the majority
>>> of current processors support it. Also, -mtune=core2 is perfectly
>>> valid as is -msse2.
>>
>> I checked that with the documentation on the Intel site and
>> the code generation options written out by the compiler (as
>> help info). On the Intel site, -msse2 and -mtune=core2 are
>> still listed as valid, whereas they aren't mentioned in the
>> help provided by the compiler I installed. Maybe they are
>> redundant with the Intel64-compiler and set by default
>> (not entirely sure). Bottom line: you are right here, I
>> missed some information.
>
> i) Indded the "-msse2" is redundant. From the icc man page:
>
> "On  Linux  systems, if neither -x nor -m is specified, the default is 
> -msse2."
>
> ii) Nope, the default as usually is -mtune=generic on "IA-32" and
> "Intel 64" - as Intel likes to call them.
>
> Btw, core2 is essentially equivalent with -xSSSE3. Depending on the
> processors you intend to run on you can try -xSSE4.1 or -xSSE4.2, but
> I doubt you'll see a noticeable difference.
>
 CMAKE_CXX_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99 '
>>>
>>> As Mark said, SSE3 won't help you in any noticeable way.
>>
>> The only 'help' I envisioned here was to avoid screen cluttering
>> by loads of warnings. mMy suggested 'fixes' weren't really fixes,
>> as I can see now. In my own development work, I can't stand
>> pages of recurring warning messages ;-) So I probably
>> overreacted here ...
>
> Sure, warnings are not nice and we dislike them as well. That's why
> these issues will be corrected in the future.
>
 But the install is broken. On `make install-mdrun`, the scripts would
 remove any library from "src/gmxlib/CMakeFiles/CMakeRelink.dir"
 and bail out with the error below. Even if you copy the libraries
 by hand to CMakeRelink.dir/, the'll get removed by make install-mdrun
 before trying to link with them.
>>>
>>> Now that is a bug. I'd appreciate if you could enter it in
>>> redmine.gromacs.org withe all details on how to reproduce it!
>>
>> I didn't do that until now but examined this further. There is already
>> an identical error posted by some other researcher (as you know):
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg39228.html
>>
>> I was able to replicate the error somehow on a different machine without
>> any intel compiler around (when building with -DGMX_MPI=ON and cmake).
>>
>> Gromacs 4.5.5: autoconf/configure on SuSE 11.4/x64 on i7
>> 
>>                 icc/64-12.1.0    gcc/x64/4.5.1
>> intThread           OK                OK
>> MPI(1.3.2)          OK                OK
>>
>>
>> Gromacs 4.5.5: cmake 2.8.3 on SuSE 11.4/x64 on i7
>> 
>>                 icc/64-12.1.0    gcc/x64/4.5.1
>> intThread          error              OK
>> MPI(1.3.2)        

[gmx-users] Slow in double-precision version

[Sai Pooja]

Hi all,

I am using GROMACS with the plugin PLUMED in double precision. The
speed has gone down by a huge margin and I was wondering if there is
something in 1) compilation 2) md parameters that could be
contributing to this?

md parameters:


title= NVT simulation (constant number, volume and
temperature)
cpp  = /lib/cpp
define   = -DPOSRES

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 500

; OUTPUT CONTROL OPTIONS
nstxout  = 0 ; ast frame (coordinates)
nstvout  = 2000   ;  (velocities)
nstfout  = 2000   ; No output, except for last frame (forces)
nstlog   = 1000  ; Write every step to the log
nstenergy= 1000  ; Write energies at every step
xtc_grps = Protein Non-Protein
nstxtcout= 500   ; Do not write a compressed trajectory
energygrps   = Protein SOL  ; Write energy information
separately for these groups
;energygrp_table  = Protein SOL SOL SOL

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 10
ns-type  = Grid
pbc  = xyz
rlist= 1.8

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Cut-off
fourierspacing   = 0.15
rcoulomb = 1.8
;rcoulomb_switch = 1.6
epsilon_rf   = 78
vdw-type = Cut-off
rvdw = 1.8
;rvdw-switch = 1.6
;table-extension = 1.0

; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
tcoupl   = nose-hoover
tc-grps  = Protein  Non-Protein
tau_t= 0.4  0.4
ref_t= 300 300

; Pressure coupling
pcoupl   = no

; OPTIONS FOR BONDS
constraints  = all-bonds


Details of the simulation:
1) MD with explicit solvent using charmm27 with tip3p (recommended one)
2) gromacs 4.5.1
3) With plumed
4) Double precision
5) Position restraints for some parts of the protein (5 chains)


I would really appreciate any help.


Regards
Pooja



Pooja

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Re: [gmx-users] Gromacs-GPU with an Nvidia GeForce GTX 580 error?

[Matt Larson]

Szilárd,

 Thanks- gromacs 4.5.5 is working with my NVidia card with the "force
option".  I found one weirdness - if I check the card temperature
(using NVIDIA's configuration tool in X11) it seems like this messes
up the MR and all the trajectories after that point have no atoms in
VMD.  So, that's probably not a good thing.

This is something of a big question:
 I tried running a simulation using intrinsic solvation, amber99 or
amber99sb, and a long helix, and found that the helix would collapse
in intrinsic solation unlike explicit solvation.  Is there a "good"
way to do intrinsic solvation simulations (like a very large # for
rvdw, rcoulomb), or some other force field such that long helices
behave well in intrinsic solvation?  It seems like the whole protein
wants scrunch up on itself.  Maybe my problem is that in the
simulation protein:protein interaction is too favored over
protein:solvent?

  Thanks,
  Matt

On Mon, Oct 24, 2011 at 2:44 PM, Szilárd Páll  wrote:
> Hi Matt,
>
> Yes, you should use the "force-device=yes" option, the patch which was
> meant to update the list of compatible GPUs didn't make it for 4.5.5.
>
> Cheers,
> --
> Szilárd
>
>
>
> On Sun, Oct 23, 2011 at 10:24 PM, Matt Larson  wrote:
>> I am having an error trying to use a compiled mdrun-gpu on my GPU setup here:
>>
>>
>> Fatal error:
>> The selected GPU (#0, GeForce GTX 580) is not supported by Gromacs!
>> Most probably you have a low-end GPU which would not perform well, or
>> new hardware that has not been tested with the current release. If you
>> still want to try using the device, use the force-device=yes option.
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> 
>>
>>  From what I can tell, the GTX 580 should be supported as of this
>> version of gromacs (4.5.5) - as it is listed in the supported cards.
>> I have openmm and CUDA libraries installed.
>>
>> - Openmm passes the test with
>> /usr/local/openmm/bin/TestReferenceHarmonicBondForce.
>> - NVIDIA driver is NVIDIA-Linux-x86_64-270.41.19
>> (devdriver_4.0_linux_64_270.41.19.run patched with the
>> nvidia_kernel-3.0-rc1.patch to let it be installed on ubuntu 11.10).
>> - the NVIDIA_GPU_Computing_SDK examples run.
>>
>>  I've also tried with the normal NVIDIA x86_64-280.13 driver, but same error.
>>
>>  From the gromacs GPU page
>> (http://www.gromacs.org/Downloads/Installation_Instructions/GPUs) it
>> is clear that the GTX 580 has been run with gromacs.
>>
>>  Should I use the "force-device" option to use GTX 580, or is there a
>> reason that gromacs doesn't think it has support for this GTX 580
>> card?
>>
>>  Thanks much,
>>  Matt Larson
>> --
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 25/10/2011 3:30 AM, James Starlight wrote:
I understand this but I've not been able found such information. I 
dont need in the most accurately  parametries for all cutt-offs of my 
system but I want to gain inside into the basic cutt- offs worked with 
the Normal mode analysis.


The cut-offs are particular to the force field, not the manner in which 
the force field is used (EM vs MD vs whatever). There are literature 
references in the GROMACS manual, and also in the published work that 
you have been reading because it has objectives similar to yours. (hint, 
hint)




E.g I've found that PME is not worked here. 


PME does work here. Last time you were apparently mis-matching files...

So I must to constrain my system with simplest cuttoffs. Could you 
provide me with the simple example e.g cutt of for interaction beetwen 
C-alpha atoms only etc?


You can't do that, and shouldn't even if you could.

Mark



James



These are particular to the force field involved, not the
software. Please consult the appropriate literature, and see what
others have used for similar work.



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Re: [gmx-users] Slow in double-precision version

[Mark Abraham]

On 25/10/2011 9:54 AM, Sai Pooja wrote:

Hi all,

I am using GROMACS with the plugin PLUMED in double precision. The
speed has gone down by a huge margin and I was wondering if there is
something in 1) compilation 2) md parameters that could be
contributing to this?


Simply moving to double precision will slow things down noticeably. How 
much depends on a lot of things, but you can test this yourself with a 
non-PLUMED double-precision GROMACS.


Otherwise, you should consider whether whatever you are doing with 
PLUMED is expected to take a lot longer than normal...




md parameters:


title= NVT simulation (constant number, volume and
temperature)
cpp  = /lib/cpp
define   = -DPOSRES

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 500

; OUTPUT CONTROL OPTIONS
nstxout  = 0 ; ast frame (coordinates)
nstvout  = 2000   ;  (velocities)
nstfout  = 2000   ; No output, except for last frame (forces)
nstlog   = 1000  ; Write every step to the log
nstenergy= 1000  ; Write energies at every step
xtc_grps = Protein Non-Protein
nstxtcout= 500   ; Do not write a compressed trajectory
energygrps   = Protein SOL  ; Write energy information
separately for these groups
;energygrp_table  = Protein SOL SOL SOL

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 10
ns-type  = Grid
pbc  = xyz
rlist= 1.8

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Cut-off
fourierspacing   = 0.15
rcoulomb = 1.8
;rcoulomb_switch = 1.6
epsilon_rf   = 78
vdw-type = Cut-off
rvdw = 1.8
;rvdw-switch = 1.6
;table-extension = 1.0

; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
tcoupl   = nose-hoover
tc-grps  = Protein  Non-Protein
tau_t= 0.4  0.4
ref_t= 300 300

; Pressure coupling
pcoupl   = no

; OPTIONS FOR BONDS
constraints  = all-bonds


Details of the simulation:
1) MD with explicit solvent using charmm27 with tip3p (recommended one)


Those cut-offs do not look like any I've ever seen for CHARMM force 
fields. It is not wise to haphazardly choose large values for poor 
electrostatic algorithms and hope for the best - even though almost all 
force fields were parameterized with poor electrostatic treatments.


Mark


2) gromacs 4.5.1
3) With plumed
4) Double precision
5) Position restraints for some parts of the protein (5 chains)


I would really appreciate any help.


Regards
Pooja



Pooja



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Re: [gmx-users] modeling cation-pi box

[Mark Abraham]

On 25/10/2011 4:20 AM, EGY wrote:

Thanks for taking the time to answer, but I think my wording may have confused my 
question. I shouldn't have used the word box. Within the protein their are several 
aromatic residues that interact with the small molecule cation. I would like to preserve 
these interactions throughout the simulations. Is it possible to "enhance" 
these interactions, since there is no defined force constants that describes these 
interactions?


Distance restraints are commonly used in proteins containing an unbound 
ion. This can keep things in place, but there's no particular reason to 
suppose it's a good model of something about which you care...


Mark


Thanks.
Egy


On Oct 24, 2011, at 12:19 PM, Justin A. Lemkul wrote:



EGY wrote:

I am interesting in modeling a small molecule ligand-protein complex that 
involves a cationic ligand encapsulated by several aromatic residues that form 
a box around the cation. However, md simulations result in the cation moving 
outside the box. I am using the CHARMM27 forcefield. Is there a way to restrain 
the cation portion of the small molecule to within the aromatic box? Or is 
there a better forcefield, which will take these interactions into 
consideration.

More than likely you simply need to account for periodicity.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin


Thanks.
Egy-- gmx-users mailing listgmx-users@gromacs.org
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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: Re: [gmx-users] failure during compiling gromacs 4.5.5

[Ye MEI]

Dear Szilárd，

Thank you very much. I removed -xHOST from CFLAGS and FFLAGS, and now it runs 
correctly.
As for Intel Compile 2011 sp1 + openmpi on my cluster, mpif90 and mpicc give 
"segmentation fault" error message.
  
Best regards,

Ye 
2011-10-25 



From： Szil醨d P醠l 
Date： 2011-10-25  03:42:17 
To： Discussion list for GROMACS users 
CC： 
Subject： Re: [gmx-users] failure during compiling gromacs 4.5.5 
 
Hi,
The error messages are all referring to SSE 4.1 packed integer min/max
operations not being recognized. I assume that these were enabled by
the "-xHOST" compiler option, and icc automatically generated these
instructions - the files it's complaining about are even temporary
files.
Could it be that you have a broken installation of Intel Compilers on
your cluster? You could check if it works if you remove -xHOST or
explicitly state -xSSE4.1.
Just for curiosity, what are the issues with the Intel Compiler 2011
(I assume that's 12.x) + OpenMPI?
Cheers,
--
Szilárd
On Mon, Oct 24, 2011 at 4:53 PM, Ye MEI  wrote:
> Dear Gromacs users,
>
> I am trying to install gromacs on my cluster using Intel Compiler 11.1.072
> and FFTW3. But I met the following error message
>  icc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 
> -I../../../include -I/usr/local/include -xHOST 
> -I/home/users/ymei/software/fftw3/intel/include -pthread -I./include -MT 
> type.lo -MD -MP -MF .deps/type.Tpo -c type.c -o type.o
> /tmp/iccLPSVQqas_.s: Assembler messages:
> /tmp/iccLPSVQqas_.s:92: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:100: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:228: Error: no such instruction: `pminsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:236: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:2559: Error: no such instruction: `pmaxsd %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:2567: Error: no such instruction: `pmaxsd 
> (%rdx,%r9,4),%xmm0'
> /tmp/iccLPSVQqas_.s:2709: Error: no such instruction: `pminsd %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:2717: Error: no such instruction: `pminsd 
> (%rdx,%r9,4),%xmm0'
> /tmp/iccLPSVQqas_.s:2989: Error: no such instruction: `pmulld %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:2997: Error: no such instruction: `pmulld 
> (%rdx,%rax,4),%xmm0'
> /tmp/iccLPSVQqas_.s:7009: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:7017: Error: no such instruction: `pmaxsb 
> (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:7145: Error: no such instruction: `pminsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:7153: Error: no such instruction: `pminsb 
> (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:9313: Error: no such instruction: `pmaxuw %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:9321: Error: no such instruction: `pmaxuw 
> (%rdx,%r9,2),%xmm0'
> /tmp/iccLPSVQqas_.s:9463: Error: no such instruction: `pminuw %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:9471: Error: no such instruction: `pminuw 
> (%rdx,%r9,2),%xmm0'
> /tmp/iccLPSVQqas_.s:10621: Error: no such instruction: `pmaxud %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:10629: Error: no such instruction: `pmaxud 
> (%rdx,%r9,4),%xmm0'
> /tmp/iccLPSVQqas_.s:10771: Error: no such instruction: `pminud %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:10779: Error: no such instruction: `pminud 
> (%rdx,%r9,4),%xmm0'
> /tmp/iccLPSVQqas_.s:11051: Error: no such instruction: `pmulld %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:11059: Error: no such instruction: `pmulld 
> (%rdx,%rax,4),%xmm0'
> /tmp/iccLPSVQqas_.s:15514: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:15522: Error: no such instruction: `pmaxsb 
> (%r8,%rdx),%xmm0'
> /tmp/iccLPSVQqas_.s:15650: Error: no such instruction: `pminsb %xmm0,%xmm1'
> /tmp/iccLPSVQqas_.s:15658: Error: no such instruction: `pminsb 
> (%r8,%rdx),%xmm0'
> make[4]: *** [type.lo] Error 1
> make[4]: Leaving directory 
> `/home/users/ymei/software/gromacs-4.5.5/src/gmxlib/thread_mpi'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory 
> `/home/users/ymei/software/gromacs-4.5.5/src/gmxlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src'
> make: *** [all-recursive] Error 1
>
> I have never seen this kind of error message before, and I donot know what
> to do to solve this problem. Can anyone help me out?
> Intel Compiler 2011 is ok. But this version does not work well with my
> cluster, especially with openmpi.
>
> And the following information might be helpful.
>
> ymei@CLOUD@ECNU:~/software/gromacs-4.5.5> gcc -v
> Using built-in specs.
> Target: x86_64-suse-linux
> Configured with: ../configure --enable-threads=posix --prefix=/usr 
> --with-local-prefix=/usr/local --infodir=/usr/share/info 
> --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 
> --enable-languages=c,c++,objc,fortran,obj-c++,java,ada 
> --enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.

Re: [gmx-users] Slow in double-precision version

[Sai Pooja]

Thank you so much Mark. You are right about the cut-off values. I am
now using 1.2nm which appears more commonly in literature. If possible
please take a look at these statistics:

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
---
 Neighbor search1 380527   166719.79259692.7 2.3
 Force  13805262  1068307.182   382498.914.8
 Write traj.1  10433 1319.463  472.4 0.0
 Update 1380526212043.902 4312.2 0.2
 Constraints1380526218769.536 6720.3 0.3
 Rest   1 5965690.942  2135968.482.5
---
 Total  1 7232850.817  2589664.9   100.0
---

   NODE (s)   Real (s)  (%)
   Time: 2476509.010 2589664.940 95.6
   28d15h55:09
   (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance: 16.281468.817  0.266 90.391
Finished mdrun on node 0 Thu Oct 13 21:43:03 2011

It seems like "Rest" option is taking 82% time. Now would this
correspond to an external program like plumed or is it something else?

Regards
Pooja


On Mon, Oct 24, 2011 at 8:18 PM, Mark Abraham  wrote:
> On 25/10/2011 9:54 AM, Sai Pooja wrote:
>>
>> Hi all,
>>
>> I am using GROMACS with the plugin PLUMED in double precision. The
>> speed has gone down by a huge margin and I was wondering if there is
>> something in 1) compilation 2) md parameters that could be
>> contributing to this?
>
> Simply moving to double precision will slow things down noticeably. How much
> depends on a lot of things, but you can test this yourself with a non-PLUMED
> double-precision GROMACS.
>
> Otherwise, you should consider whether whatever you are doing with PLUMED is
> expected to take a lot longer than normal...
>
>>
>> md parameters:
>>
>>
>> title                    = NVT simulation (constant number, volume and
>> temperature)
>> cpp                      = /lib/cpp
>> define                   = -DPOSRES
>>
>> ; RUN CONTROL PARAMETERS
>> integrator               = md
>> dt                       = 0.002
>> nsteps                   = 500
>>
>> ; OUTPUT CONTROL OPTIONS
>> nstxout                  = 0 ; ast frame (coordinates)
>> nstvout                  = 2000   ;  (velocities)
>> nstfout                  = 2000   ; No output, except for last frame
>> (forces)
>> nstlog                   = 1000  ; Write every step to the log
>> nstenergy                = 1000  ; Write energies at every step
>> xtc_grps                 = Protein Non-Protein
>> nstxtcout                = 500   ; Do not write a compressed trajectory
>> energygrps               = Protein SOL  ; Write energy information
>> separately for these groups
>> ;energygrp_table          = Protein SOL SOL SOL
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> nstlist                  = 10
>> ns-type                  = Grid
>> pbc                      = xyz
>> rlist                    = 1.8
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> coulombtype              = Cut-off
>> fourierspacing           = 0.15
>> rcoulomb                 = 1.8
>> ;rcoulomb_switch         = 1.6
>> epsilon_rf               = 78
>> vdw-type                 = Cut-off
>> rvdw                     = 1.8
>> ;rvdw-switch             = 1.6
>> ;table-extension                 = 1.0
>>
>> ; FFT grid size, when a value is 0 fourierspacing will be used =
>> fourier_nx               = 0
>> fourier_ny               = 0
>> fourier_nz               = 0
>> ; EWALD/PME/PPPM parameters =
>> pme_order                = 4
>> ewald_rtol               = 1e-05
>> epsilon_surface          = 0
>> optimize_fft             = no
>> ; Temperature coupling
>> tcoupl                   = nose-hoover
>> tc-grps                  = Protein  Non-Protein
>> tau_t                    = 0.4      0.4
>> ref_t                    = 300 300
>>
>> ; Pressure coupling
>> pcoupl                   = no
>>
>> ; OPTIONS FOR BONDS
>> constraints              = all-bonds
>>
>>
>> Details of the simulation:
>> 1) MD with explicit solvent using charmm27 with tip3p (recommended one)
>
> Those cut-offs do not look like any I've ever seen for CHARMM force fields.
> It is not wise to haphazardly choose large values for poor electrostatic
> algorithms and hope for the best - even though almost all force fields were
> parameterized with poor electrostatic treatments.
>
> Mark
>
>> 2) gromacs 4.5.1
>> 3) With plumed
>> 4) Double precision
>> 5) Position restraints for some parts of the protein (5 chains)
>>
>>
>> I would really appreciate any help.
>>
>>
>> Regards
>> Pooja
>>
>>
>>
>> Pooja
>>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/

Re: [gmx-users] Slow in double-precision version

[Mark Abraham]

On 25/10/2011 3:11 PM, Sai Pooja wrote:

Thank you so much Mark. You are right about the cut-off values. I am
now using 1.2nm which appears more commonly in literature. If possible
please take a look at these statistics:

  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

  Computing: Nodes Number G-CyclesSeconds %
---
  Neighbor search1 380527   166719.79259692.7 2.3
  Force  13805262  1068307.182   382498.914.8
  Write traj.1  10433 1319.463  472.4 0.0
  Update 1380526212043.902 4312.2 0.2
  Constraints1380526218769.536 6720.3 0.3
  Rest   1 5965690.942  2135968.482.5
---
  Total  1 7232850.817  2589664.9   100.0
---

NODE (s)   Real (s)  (%)
Time: 2476509.010 2589664.940 95.6
28d15h55:09
(Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance: 16.281468.817  0.266 90.391
Finished mdrun on node 0 Thu Oct 13 21:43:03 2011

It seems like "Rest" option is taking 82% time. Now would this
correspond to an external program like plumed


Yep. "rest" is a catch-all, and plumed is probably not anywhere else. 
Their developers would be able to tell you.


Mark


or is it something else?

Regards
Pooja


On Mon, Oct 24, 2011 at 8:18 PM, Mark Abraham  wrote:

On 25/10/2011 9:54 AM, Sai Pooja wrote:

Hi all,

I am using GROMACS with the plugin PLUMED in double precision. The
speed has gone down by a huge margin and I was wondering if there is
something in 1) compilation 2) md parameters that could be
contributing to this?

Simply moving to double precision will slow things down noticeably. How much
depends on a lot of things, but you can test this yourself with a non-PLUMED
double-precision GROMACS.

Otherwise, you should consider whether whatever you are doing with PLUMED is
expected to take a lot longer than normal...


md parameters:


title= NVT simulation (constant number, volume and
temperature)
cpp  = /lib/cpp
define   = -DPOSRES

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 500

; OUTPUT CONTROL OPTIONS
nstxout  = 0 ; ast frame (coordinates)
nstvout  = 2000   ;  (velocities)
nstfout  = 2000   ; No output, except for last frame
(forces)
nstlog   = 1000  ; Write every step to the log
nstenergy= 1000  ; Write energies at every step
xtc_grps = Protein Non-Protein
nstxtcout= 500   ; Do not write a compressed trajectory
energygrps   = Protein SOL  ; Write energy information
separately for these groups
;energygrp_table  = Protein SOL SOL SOL

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 10
ns-type  = Grid
pbc  = xyz
rlist= 1.8

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Cut-off
fourierspacing   = 0.15
rcoulomb = 1.8
;rcoulomb_switch = 1.6
epsilon_rf   = 78
vdw-type = Cut-off
rvdw = 1.8
;rvdw-switch = 1.6
;table-extension = 1.0

; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
tcoupl   = nose-hoover
tc-grps  = Protein  Non-Protein
tau_t= 0.4  0.4
ref_t= 300 300

; Pressure coupling
pcoupl   = no

; OPTIONS FOR BONDS
constraints  = all-bonds


Details of the simulation:
1) MD with explicit solvent using charmm27 with tip3p (recommended one)

Those cut-offs do not look like any I've ever seen for CHARMM force fields.
It is not wise to haphazardly choose large values for poor electrostatic
algorithms and hope for the best - even though almost all force fields were
parameterized with poor electrostatic treatments.

Mark


2) gromacs 4.5.1
3) With plumed
4) Double precision
5) Position restraints for some parts of the protein (5 chains)


I would really appreciate any help.


Regards
Pooja



Pooja


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Re: [gmx-users] Lyzosyme with ligand tutorial

[James Starlight]

This was due to that in .gro file corresponded to the end of productive MD
I've found this http://i1209.photobucket.com/albums/cc394/own11/mdL.png
It's looks like the protein moved out from box so I've thought that some
error occured during stimulation


>>
> I don't understand this statement.  You should also note that a periodic
> box has no "outside."  Perhaps it would be useful to post images online.  If
> you choose to do so, please follow bullet point #4 here:
>
> http://www.gromacs.org/**Support/Mailing_Lists#Mailing_**List_Etiquette
>
>
> -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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