date:20130815




On 8/15/13 3:05 PM, Bin Liu wrote:

Hi All,

I am simulating a system of lipopeptides embedded into a lipid bilayer. I
have a question about how g_membed works.

My bilayer has three kinds of lipids. Let's call them lipid_1, lipid_2,
lipid_3. Sodium ions are used to balance the charges. When I invoke
g_membed, it will ask for which group to embed in the membrane. In my case,
obviously it is the group Lipopeptide. Then g_membed asks for a group to
embed Lipopeptide into. Should it be the joint group of lipid_1, lipid_2
and lipid_3? Or something else?

I used make_ndx to generate an index group called Membrane by merging group
Lipid_1, Lipid_2 and Lipid_3. It seems it works with g_membed. It gives the
following information:

Will remove 2 Lipid_1 molecules
Will remove 1 Lipid_2 molecules
Will remove 3 Lipid_3 molecules
Will remove 7 SOL molecules
Will remove 0 NA molecules
Will remove 0 Lipopeptide molecules

Apparently the behaviour of g_membed is what I want. But what concerns me
is I don't know whether the removal of 0 Sodium ions is just a coincidence
or it's a deterministic action by g_membed. Of course I don't want the
removal of ions as it would cause a charged system. So my question is under
what conditions will g_membed remove ions?



Whenever you delete molecules from a system, there will have to be corresponding 
changes in the topology, some that may require you to re-calculate the number of 
ions you need.  Molecules are deleted simply based on physical overlap.  Full 
details are in the g_membed paper (dx.doi.org/10.1002/jcc.21507).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] for help about reading xtc file

2013-08-15 Thread Xu, Yechuan

Thank you for your reply. after I read the xdrfile.c, 

I changed the sentence as
pos=xdr_getpos((XDR*) (xtc->xdr));

like that in the file of xdrfile.c. I also copy the definition 
for XDR and xdr_op to my own code.

But I still got the errors:
seekxtc.c:61:33: error: dereferencing pointer to incomplete type
   pos=xdr_getpos((XDR *)(xtc->xdr));
^

here are my code:
#include 
#include 
#include 
#include 

enum xdr_op
{
   XDR_ENCODE = 0,
   XDR_DECODE = 1,
   XDR_FREE   = 2
};

typedef struct XDR XDR; 

struct XDR
{
   enum xdr_op x_op;
   struct xdr_ops
   {
  int (*x_getlong) (XDR *__xdrs, int32_t *__lp);
  int (*x_putlong) (XDR *__xdrs, int32_t *__lp);
  int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
  int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
  /* two next routines are not 64-bit IO safe - don't use! */
  unsigned int (*x_getpostn) (XDR *__xdrs); 
  int (*x_setpostn) (XDR *__xdrs, unsigned int __pos);
  void (*x_destroy) (XDR *__xdrs); 
   }
   *x_ops;  
   char *x_private;
};


int main(int argc, char *argv[])
{
   int i; 
   int step, read_return, result;
   int natoms;
   float time,prec=1000.;
   matrix box;
   rvec *x;
   XDRFILE *xtc;
   char *fname;
   unsigned int pos;

   printf("begin, argc=%d\n",argc);
   if(argc==2){
  fname=argv[1];
   }

   xtc=xdrfile_open (fname,"r");
   read_xtc_natoms (fname,&natoms);
   printf("number of atoms: %d\n",natoms);

   x = calloc(natoms, sizeof (x[0]));

   while(1){
  read_return=read_xtc(xtc,natoms,&step,&time,box,x,&prec);
  if (read_return!=0) break;

  pos=xdr_getpos((XDR *)(xtc->xdr));
  printf("%d\n",pos);

   }

   xdrfile_close (xtc);
}
Thanks,
YC


On Aug 15, 2013, at 3:09 PM, Mark Abraham wrote:

> Right, because a pointer to an XDRFILE is neither a struct nor a union
> :-) Look at how these routines are used, and consult the header files
> for the right types to give them.
> 
> Mark
> 
> On Thu, Aug 15, 2013 at 7:29 PM, Xu, Yechuan  wrote:
>> Hi Everyone,
>> 
>> I want to read a certain frame in a xtc file. How can I do that?
>> I see there are xdr_getpos() and xdr_setpos(). How should I use
>> these functions?
>> 
>> I tried:
>> 
>> XDRFILE *xtc;
>> unsigned int pos;
>> 
>> pos=xdr_getpos(xtc.xdr);
>> 
>> but I got:
>> error: request for member ‘xdr’ in something not a structure or union
>> 
>> Thanks in advance.
>> YC--
>> 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!
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>> www interface or send it to gmx-users-requ...@gromacs.org.
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> -- 
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Re: [gmx-users] LINCS Constraints - all-bonds or h-bonds?

2013-08-15 Thread Michael Shirts

I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic 
energy start being subtly off.

H-bonds has less chance of failing with large numbers of constraints- less 
iteration required, especially if bond system cross parallelization boundaries.

If your molecules are < 10 atoms, it probably doesn't matter either way.

Sent from my iPhone

On Aug 15, 2013, at 9:11, "Barnett, James W."  wrote:

> Searching through this mailing list it seems like some have stated that 
> with a 2 fs timestep (dt=0.002), constraints=h-bonds is fine in general.
> 
> The questions I have are:
> 
> 1) What are some personal opinions on when it is ok to switch to h-bonds 
>   from all-bonds for LINCS constraints? Is 2 fs and h-bonds a general 
> practice?
> 
> 2) Also, if typically 2 fs and h-bonds are ok, what time-step do users 
>   (or you personally) generally go to with all-bonds? 
> 
> I am speaking generally here of course. Thanks for your responses.
> 
> -- 
> Wes Barnett | jbarn...@tulane.edu
> 
> -- 
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Re: [gmx-users] for help about reading xtc file

Right, because a pointer to an XDRFILE is neither a struct nor a union
:-) Look at how these routines are used, and consult the header files
for the right types to give them.

Mark

On Thu, Aug 15, 2013 at 7:29 PM, Xu, Yechuan  wrote:
> Hi Everyone,
>
> I want to read a certain frame in a xtc file. How can I do that?
> I see there are xdr_getpos() and xdr_setpos(). How should I use
> these functions?
>
> I tried:
>
> XDRFILE *xtc;
> unsigned int pos;
>
> pos=xdr_getpos(xtc.xdr);
>
> but I got:
> error: request for member ‘xdr’ in something not a structure or union
>
> Thanks in advance.
> YC--
> 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!
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[gmx-users] Molecule removal by g_membed

2013-08-15 Thread Bin Liu

Hi All,

I am simulating a system of lipopeptides embedded into a lipid bilayer. I
have a question about how g_membed works.

My bilayer has three kinds of lipids. Let's call them lipid_1, lipid_2,
lipid_3. Sodium ions are used to balance the charges. When I invoke
g_membed, it will ask for which group to embed in the membrane. In my case,
obviously it is the group Lipopeptide. Then g_membed asks for a group to
embed Lipopeptide into. Should it be the joint group of lipid_1, lipid_2
and lipid_3? Or something else?

I used make_ndx to generate an index group called Membrane by merging group
Lipid_1, Lipid_2 and Lipid_3. It seems it works with g_membed. It gives the
following information:

Will remove 2 Lipid_1 molecules
Will remove 1 Lipid_2 molecules
Will remove 3 Lipid_3 molecules
Will remove 7 SOL molecules
Will remove 0 NA molecules
Will remove 0 Lipopeptide molecules

Apparently the behaviour of g_membed is what I want. But what concerns me
is I don't know whether the removal of 0 Sodium ions is just a coincidence
or it's a deterministic action by g_membed. Of course I don't want the
removal of ions as it would cause a charged system. So my question is under
what conditions will g_membed remove ions?

Thank you in advance.

Regards

Bin
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[gmx-users] for help about reading xtc file

2013-08-15 Thread Xu, Yechuan

Hi Everyone,

I want to read a certain frame in a xtc file. How can I do that?
I see there are xdr_getpos() and xdr_setpos(). How should I use
these functions?

I tried:

XDRFILE *xtc;
unsigned int pos;

pos=xdr_getpos(xtc.xdr);

but I got:
error: request for member ‘xdr’ in something not a structure or union

Thanks in advance.
YC--
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Re: [gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names?

2013-08-15 Thread Joerg Sauter


Hi Mark,

Using -rtpres also doesn't work.

Since this happens only with a specbond.dat present there could be a 
note when using specbond.dat.


Since usually mixed residues (looking for BGLE atoms in BGLM rtp) should 
not occur when this fatal error is thrown (?), a more specific 
alternative might be to have an additional check for mixed residues and, 
in case, an additional warning to the fatal error (like in the case of 
missing hydrogen).


Best,
Joerg


On 15.08.2013 18:07, Mark Abraham wrote:

It's not clear whether this is or should be an intended behaviour.
There are lots of considerations of atom and residue renaming that
pdb2gmx tries to handle, and it is not too surprising that there are
corner cases that don't work as everyone expects. I couldn't even find
the code where this might happen. You might have been able to avoid
renaming your .rtp entries manually by using pdb2gmx -rtpres.

Where would have been a good place for you to have read "Using
three-letter .rtp residue names might make life easier. Consider using
pdb2gmx -rtpres if you need longer names."

Mark

On Thu, Aug 15, 2013 at 3:45 PM, Joerg Sauter  wrote:

Hi,

I am building a tetramer of beta(1-4) linked glucose with pdb2gmx (Gromacs
4.6.3). I have three residue types BGLB BGLM BGLE defined in the
aminoacids.rtp with which I want to built the chain BGLB BGLM BGLM BGLE.

Using pdb2gmx works fine, until I link the residues via the specbond.dat
file:

3
BGLBO41BGLMC110.147 BGLBBGLM
BGLMO41BGLMC110.147 BGLMBGLM
BGLMO41BGLEC110.147 BGLMBGLE

In this case I get the error message:

Fatal error:
Atom HO4 in residue BGLE 4 was not found in rtp entry BGLM with 21 atoms
while sorting atoms.

Using the -debug 1 mode I found that internally (in the chain.pdb) the
residue names get shortened to BGL thus making the residues
indistinguishable. Therefore, pdb2gmx seems to mix up residues resulting in
the error above. If I use residue names consisting of only 3 characters
everything works fine again.

Is this behaviour known or intended? I could not find any note on this in
the manual and it took me some time to figure this out, so maybe there
should be at least a warning.

Best,
Joerg

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--
Joerg Sauter
Max Planck Institute of Colloids and Interfaces
Department of Theory & Bio-Systems
Am Mühlenberg 1
14476 Potsdam-Golm Germany

Fon: +49-(0)331-567-9622

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Re: [gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names?

It's not clear whether this is or should be an intended behaviour.
There are lots of considerations of atom and residue renaming that
pdb2gmx tries to handle, and it is not too surprising that there are
corner cases that don't work as everyone expects. I couldn't even find
the code where this might happen. You might have been able to avoid
renaming your .rtp entries manually by using pdb2gmx -rtpres.

Where would have been a good place for you to have read "Using
three-letter .rtp residue names might make life easier. Consider using
pdb2gmx -rtpres if you need longer names."

Mark

On Thu, Aug 15, 2013 at 3:45 PM, Joerg Sauter  wrote:
> Hi,
>
> I am building a tetramer of beta(1-4) linked glucose with pdb2gmx (Gromacs
> 4.6.3). I have three residue types BGLB BGLM BGLE defined in the
> aminoacids.rtp with which I want to built the chain BGLB BGLM BGLM BGLE.
>
> Using pdb2gmx works fine, until I link the residues via the specbond.dat
> file:
>
> 3
> BGLBO41BGLMC110.147 BGLBBGLM
> BGLMO41BGLMC110.147 BGLMBGLM
> BGLMO41BGLEC110.147 BGLMBGLE
>
> In this case I get the error message:
>
> Fatal error:
> Atom HO4 in residue BGLE 4 was not found in rtp entry BGLM with 21 atoms
> while sorting atoms.
>
> Using the -debug 1 mode I found that internally (in the chain.pdb) the
> residue names get shortened to BGL thus making the residues
> indistinguishable. Therefore, pdb2gmx seems to mix up residues resulting in
> the error above. If I use residue names consisting of only 3 characters
> everything works fine again.
>
> Is this behaviour known or intended? I could not find any note on this in
> the manual and it took me some time to figure this out, so maybe there
> should be at least a warning.
>
> Best,
> Joerg
>
> --
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Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

2013-08-15 Thread Richard Broadbent

Dear Grita,

\sigma in gromacs is the value of \sigma in a Lennard-Jones (LJ)
potential defined by:

4\epsilon*[(sigma/r)^12-(sigma/r)^6],
where r is the separation between the two point particles, epsilon is
the well depth, and \sigma is a length scale which characterises the
interaction between two particles. This is the same as in the wikipedia
article Justin linked to or numerous other websites, journal articles,
and text books discussing the LJ potential.

The particles if they have sufficient energy can move closer than \sigma
together or they can move further apart than \sigma.

As Justin said there is no such thing as a particles diameter in gromacs
everything is a point particle with no radius or diameter.

If you want something where the particles absolutely cannot overlap
regardless of their energy you will need to consider hard-sphere
potentials. However, as these are not continuous and therefore not
really suited to MD simulations I doubt that's what you want.

Richard

On 15/08/13 14:26, grita wrote:

Hi Justin,

yes, the LJ potential is zero when the two spheres are at a separation of 5
angstrom.

So, I can be sure, that in this case the \sigma in

c^6 = 4 \epsilon \sigma^6
c^12 = 4 \epsilon \sigma^12

are the seperation or 'my interaction diameter / interaction distance'???

I've asked for this, because in other force fields there are different
definitions of sigma.

Sorry for the confusion.

In short, the sigma is the separation or the 'diameter'. True or False ???

Best, grita

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[gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names?

2013-08-15 Thread Joerg Sauter


Hi,

I am building a tetramer of beta(1-4) linked glucose with pdb2gmx 
(Gromacs 4.6.3). I have three residue types BGLB BGLM BGLE defined in 
the aminoacids.rtp with which I want to built the chain BGLB BGLM BGLM BGLE.


Using pdb2gmx works fine, until I link the residues via the specbond.dat 
file:


3
BGLBO41BGLMC110.147 BGLBBGLM
BGLMO41BGLMC110.147 BGLMBGLM
BGLMO41BGLEC110.147 BGLMBGLE

In this case I get the error message:

Fatal error:
Atom HO4 in residue BGLE 4 was not found in rtp entry BGLM with 21 atoms
while sorting atoms.

Using the -debug 1 mode I found that internally (in the chain.pdb) the 
residue names get shortened to BGL thus making the residues 
indistinguishable. Therefore, pdb2gmx seems to mix up residues resulting 
in the error above. If I use residue names consisting of only 3 
characters everything works fine again.


Is this behaviour known or intended? I could not find any note on this 
in the manual and it took me some time to figure this out, so maybe 
there should be at least a warning.


Best,
Joerg

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[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Hi Justin,

yes, the LJ potential is zero when the two spheres are at a separation of 5
angstrom.

So, I can be sure, that in this case the \sigma in

c^6 = 4 \epsilon \sigma^6
c^12 = 4 \epsilon \sigma^12

are the seperation or 'my interaction diameter / interaction distance'???

I've asked for this, because in other force fields there are different
definitions of sigma.

Sorry for the confusion.

In short, the sigma is the separation or the 'diameter'. True or False ???

Best, grita





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[gmx-users] LINCS Constraints - all-bonds or h-bonds?

2013-08-15 Thread Barnett, James W.

Searching through this mailing list it seems like some have stated that 
with a 2 fs timestep (dt=0.002), constraints=h-bonds is fine in general.

The questions I have are:

1) What are some personal opinions on when it is ok to switch to h-bonds 
   from all-bonds for LINCS constraints? Is 2 fs and h-bonds a general 
practice?

2) Also, if typically 2 fs and h-bonds are ok, what time-step do users 
   (or you personally) generally go to with all-bonds? 

I am speaking generally here of course. Thanks for your responses.

-- 
Wes Barnett | jbarn...@tulane.edu

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Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?




On 8/15/13 8:58 AM, grita wrote:

Hi,

with "interaction diameter" I mean the following:

I have two spheres with a radii of 2.5 angstrom.
The spheres should not overlap.


From that, I derive my 'interaction diameter'/'interaction distance' 5

angstrom.

Now, the 5 angstroms should be the \sigma in the following formulas


c^6 = 4 \epsilon \sigma^6
c^12 = 4 \epsilon \sigma^12


Is it so?



It's still not entirely clear.  Is the value of the LJ potential zero when the 
two spheres are at a 5-A separation?  If it is, then that's the value of sigma. 
 If the 5-A separation defines the energy minimum for the interaction between 
the two particles, then that's not sigma, the 5 A value would be r_m, from which 
sigma can be calculated.  None of this guarantees that the spheres will not 
overlap, given the form of the LJ potential.


-Justin

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[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Hi,

with "interaction diameter" I mean the following:

I have two spheres with a radii of 2.5 angstrom.
The spheres should not overlap.

>From that, I derive my 'interaction diameter'/'interaction distance' 5
angstrom.

Now, the 5 angstroms should be the \sigma in the following formulas

> c^6 = 4 \epsilon \sigma^6
> c^12 = 4 \epsilon \sigma^12 

Is it so?

Best, grita



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Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

2013-08-15 Thread massimo sandal

You have to define what do you mean by "interaction diameter".


2013/8/15 grita 

> Hi Justin,
>
> thanks for your help.
>
> What I want to understand is the following:
>
> I have two particles and the interaction diameter should be 5 angstroms.
>
> The \sigma in this formulas
>
> c^6 = 4 \epsilon \sigma^6
> c^12 = 4 \epsilon \sigma^12
>
> would be 5, or?
>
> Best, grita
>
>
>
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[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Hi Justin,

thanks for your help.

What I want to understand is the following:

I have two particles and the interaction diameter should be 5 angstroms.

The \sigma in this formulas

c^6 = 4 \epsilon \sigma^6
c^12 = 4 \epsilon \sigma^12

would be 5, or?

Best, grita



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Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?




On 8/15/13 8:28 AM, grita wrote:

Hi Justin,

Wikipedia says: "sigma is the finite distance at which the inter-particle
potential is zero"

But if I want to simulate particles with a certain diameter, where can I set
the diameter in Gromcas?.
For example, a sphere with a diameter of 5 angstroms, would then sigma 5
angstroms?



No.  There are no explicit settings for particle size anywhere in Gromacs (with 
the possible exception of vdwradii.dat, but that's only used by genbox and 
g_sas).  Dynamics rely on inter-particle potentials.  You would have to derive 
and/or tune parameters that represent physical reality of what a particle's size 
should be such that it is reflected in the outcome of MD.


-Justin

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[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Hi Justin,

Wikipedia says: "sigma is the finite distance at which the inter-particle
potential is zero"

But if I want to simulate particles with a certain diameter, where can I set
the diameter in Gromcas?.
For example, a sphere with a diameter of 5 angstroms, would then sigma 5
angstroms?

Best,
grita



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Re: [gmx-users] what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?




On 8/15/13 7:59 AM, grita wrote:

Hi,

can someone tell me exactly what the \sigma in the LJ-potential in Gromacs
is?

Is \sigma the radius of a sphere or the diameter of a sphere?



Neither.

http://en.wikipedia.org/wiki/Lennard-Jones_potential

-Justin

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[gmx-users] what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Hi,

can someone tell me exactly what the \sigma in the LJ-potential in Gromacs
is?

Is \sigma the radius of a sphere or the diameter of a sphere?

I am not so sure, because I want to calculate the parameters

c^6 = 4 \epsilon \sigma^6
c^12 = 4 \epsilon \sigma^12.

Best,
grita



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Re: [gmx-users] Running g_tune_pme on a BlueGene/Q cluster

export MPIRUN=$(which srun) should be all you need to help g_tune_pme
to understand how to start an MPI calc. g_tune_pme runs in serial, but
it needs to *call* srun.

Mark

On Thu, Aug 15, 2013 at 11:46 AM, Jernej Zidar  wrote:
> Hi,
>   I would like to determine the optimum number of PP/PME nodes to be
> used for my simulation. I found the tool g_tune_pme can be used.
>   The cluster is a BlueGene/Q machine using SLUR as the scheduler. I
> tried using the following scirpt:
> !/bin/bash
> #SBATCH --time=1:00:00
> #SBATCH --nodes=16
> #SBATCH --ntasks-per-node=16
> #SBATCH -J "tune"
> #SBATCH -o "tuning.out"
> #SBATCH -p "normal"
> file=my_tpr_file
> source /home/ihpczidj/scratch/gromacs-4.6.3-bgq/bin/GMXRC
> export MDRUN="/home/ihpczidj/scratch/gromacs-4.6.3-bgq/bin/mdrun"
> srun g_tune_pme -np 256 -s "$file" -steps 1000 -ntpr 1
>
> - - - -
>   But it didn't work:
> Program g_tune_pme, VERSION 4.6.3
> Source code file:
> /home/ihpczidj/scratch/gromacs-4.6.3/src/tools/gmx_tune_pme.c, line:
> 665
>
> Fatal error:
> Output from test run could not be found.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>   Any suggestions? I'm trying to find the location of the 'srun'
> wrapper but I'm unable to find it.
>
> Thanks,
> Jernej
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[gmx-users] Running g_tune_pme on a BlueGene/Q cluster

2013-08-15 Thread Jernej Zidar

Hi,
  I would like to determine the optimum number of PP/PME nodes to be
used for my simulation. I found the tool g_tune_pme can be used.
  The cluster is a BlueGene/Q machine using SLUR as the scheduler. I
tried using the following scirpt:
!/bin/bash
#SBATCH --time=1:00:00
#SBATCH --nodes=16
#SBATCH --ntasks-per-node=16
#SBATCH -J "tune"
#SBATCH -o "tuning.out"
#SBATCH -p "normal"
file=my_tpr_file
source /home/ihpczidj/scratch/gromacs-4.6.3-bgq/bin/GMXRC
export MDRUN="/home/ihpczidj/scratch/gromacs-4.6.3-bgq/bin/mdrun"
srun g_tune_pme -np 256 -s "$file" -steps 1000 -ntpr 1

- - - -
  But it didn't work:
Program g_tune_pme, VERSION 4.6.3
Source code file:
/home/ihpczidj/scratch/gromacs-4.6.3/src/tools/gmx_tune_pme.c, line:
665

Fatal error:
Output from test run could not be found.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

  Any suggestions? I'm trying to find the location of the 'srun'
wrapper but I'm unable to find it.

Thanks,
Jernej
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Re: [gmx-users] GPU metadynamics

2013-08-15 Thread Albert


On 08/15/2013 11:21 AM, Jacopo Sgrignani wrote:

Dear Albert
to run parallel jobs on multiple GPUs you should use something like this:

mpirun -np (number of parallel sessions on CPU) mdrun_mpi .. -gpu_id 


so you will have 4 calculations for GPU.


Jacopo


thanks a  lot for reply. but there is some problem with following command:

mpirun -np 4 mdrun_mpi -s md.tpr -v -g md.log -o md.trr -x md.xtc 
-plumed plumed2.dat -e md.edr -gpu_id 0123.


--log---

4 GPUs detected on host node3:
  #0: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
  #1: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
  #2: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
  #3: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible


---
Program mdrun_mpi, VERSION 4.6.3
Source code file: 
/home/albert/install/source/gromacs-4.6.3/src/gmxlib/gmx_detect_hardware.c, 
line: 349


Fatal error:
Incorrect launch configuration: mismatching number of PP MPI processes 
and GPUs per node.
mdrun_mpi was started with 1 PP MPI process per node, but you provided 4 
GPUs.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

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Re: [gmx-users] GPU metadynamics

2013-08-15 Thread Jacopo Sgrignani

Dear Albert
to run parallel jobs on multiple GPUs you should use something like this:

mpirun -np (number of parallel sessions on CPU) mdrun_mpi .. -gpu_id 


so you will have 4 calculations for GPU.


Jacopo

Inviato da iPad

Il giorno 15/ago/2013, alle ore 10:56, Albert  ha scritto:

> Hello:
> 
> I've got two GTX690 GPU in a workstation, and I compiled gromacs-4.6.3 with 
> plumed and MPI support. I am trying to run some metadynamics with mdrun with 
> command:
> 
> mdrun_mpi -s md.tpr -v -g md.log -o md.trr -x md.xtc -plumed plumed2.dat -e 
> md.edr
> 
> but mdrun can only use 1 GPU as indicated in the log file:
> 
> 
> 
> 4 GPUs detected on host node3:
>  #0: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
>  #1: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
>  #2: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
>  #3: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
> 
> 
> NOTE: potentially sub-optimal launch configuration, mdrun_mpi started with 
> less
>  PP MPI process per node than GPUs available.
>  Each PP MPI process can use only one GPU, 1 GPUs per node will be used.
> 
> 1 GPU auto-selected for this run: #0
> 
> 
> 
> I am just wondering how can we use multiple GPU for such kind of jobs?
> 
> THX
> Albert
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[gmx-users] GPU metadynamics

2013-08-15 Thread Albert


Hello:

 I've got two GTX690 GPU in a workstation, and I compiled gromacs-4.6.3 
with plumed and MPI support. I am trying to run some metadynamics with 
mdrun with command:


 mdrun_mpi -s md.tpr -v -g md.log -o md.trr -x md.xtc -plumed 
plumed2.dat -e md.edr


but mdrun can only use 1 GPU as indicated in the log file:



4 GPUs detected on host node3:
  #0: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
  #1: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
  #2: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
  #3: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible


NOTE: potentially sub-optimal launch configuration, mdrun_mpi started 
with less

  PP MPI process per node than GPUs available.
  Each PP MPI process can use only one GPU, 1 GPUs per node will be 
used.


1 GPU auto-selected for this run: #0



I am just wondering how can we use multiple GPU for such kind of jobs?

THX
Albert
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Re: [gmx-users] plans for mdrun features to deprecate in GROMACS 5.0

On Wed, Aug 14, 2013 at 10:17 PM, rajat desikan  wrote:
> I am interested in Generalized Born. My coding skills are limited, but I
> would like to help to whatever extent I can.

Big issues at the moment are that both the "all vs all" and
SIMD-accelerated GB kernels are broken in 4.6.x but worked in 4.5.x
(see http://redmine.gromacs.org/issues/1249). That probably means that
performance of the plain-C kernels is lower than a similar
explicit-solvent system. I expect that the problem is not severe -
just that some assumption in the GB kernel or setup code has been
violated during the changes leading to 4.6. If you're keen, those
would be useful things to have working!

> I am also interested in helping towards revamping the tutorials if the need
> should arise.

There are several tutorials under preparation for the GROMACS workshop
in Virginia in September. I'm sure some preliminary feedback on those
would be welcome when they're ready!

Thanks!

Mark

> On Wed, Aug 14, 2013 at 8:36 PM, Mark Abraham wrote:
>
>> Hi gmx-users and gmx-developers,
>>
>> There are a number of features of GROMACS that we plan to drop for 5.0
>> (scheduled for early 2014). We don’t like doing this, but if things
>> are broken or cause developers pain, then they will go unless there is
>> manpower to support them. We’d like to keep you informed and hear how
>> much pain any of this might cause. Some features will be dropped
>> entirely, and others are likely to be reduced to explicit support only
>> for some cases. Some discussion has already occurred here
>> http://redmine.gromacs.org/issues/1292.
>>
>> Things we plan to drop entirely:
>> * particle decomposition (see below)
>> * current QM support (this will be dropped, work on a replacement is
>> underway, planned for 5.0)
>> * writing of pair distance and/or time-averaged pair distance to
>> energy files during simulations with position/orientation restraints
>> * reaction-field-nec
>> * Encad-shift
>> * mdrun -ionize
>> * GCT
>> * mdrun -seppot
>> * mdrun -ffscan
>> * OpenMM support
>>
>> There are several algorithms (e.g. fancy kinds of restraints) that
>> have only ever worked with particle decomposition (if they work at
>> all...). We plan to support these only in serial.
>>
>> Things that will likely only work in serial (ie. single-domain DD):
>> * ensemble- and time-averaged distance restraints
>> * L-BFGS energy minimization
>> * Generalized Born
>>
>> In some cases, “in serial” might mean “in parallel (with DD) with an
>> extra communication stage that will make it work, but might scale
>> poorly.” Or “in parallel but if things diffuse too far, the simulation
>> will crash.” If you have working examples of any of the above in
>> parallel, we would be most interested to hear from you. We’d like to
>> construct test cases that show what works now, so that later if we are
>> able to support some kind of parallelism, we can show that it still
>> works.
>>
>> Things that won’t support constraints (because the implementations are
>> broken or missing):
>> * L-BFGS energy minimization
>> * MTTK pressure coupling
>>
>> As always, what goes into GROMACS depends on people putting the work
>> in. If something above would affect you, then do speak up.
>> Contributions of working test cases are particularly valuable, but in
>> the end you might have to be the one to write the code to make the
>> test pass. You will have the option of continuing to use old code,
>> too!
>>
>> Cheers,
>>
>> Mark
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>
>
>
> --
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> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
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Re: [gmx-users] VDW switched off in CHARMM tip3p model