[gmx-users] Intel Compiler Options on Itanium2

Erik Lindahl lindahl at csb.stanford.edu
Mon Jan 26 21:16:01 CET 2004 

Hi Marc,

This should be automatic in 3.2, although I fixed a bug so the beta  
might not detect them correctly. Justin is checking one remaining bug  
in the pull package, so I hope for a release tomorrow.

There isn't much to play around with on ia64; I've tested lots of  
things but they don't have much effect. Use

CFLAGS="-O3"
FFLAGS="-O3 -w90 -w95"

The extra fortran flags just turn off all warnings that are generated  
for Fortran77 source (ifort is F95 by default).

Cheers,

Erik


On Jan 26, 2004, at 8:54 PM, Marc Ceruso wrote:

> Hi,
> Does any one have suggestions for compiler options (CFLAGS) to compile
> gromacs on a itanium2 with intel compiler ifort and icc (version 8.0)?
> Thanks
>
>> -----Original Message-----
>> From: gmx-users-admin at gromacs.org  
>> [mailto:gmx-users-admin at gromacs.org]On
>> Behalf Of Ilya Chorny
>> Sent: Sunday, January 25, 2004 1:01 AM
>> To: gmx-users at gromacs.org
>> Subject: RE: [gmx-users] cutt offs
>>
>>
>> I want to calc the solvation free enenrgy of large lennard jones  
>> spheres
>> with radius's of 10-15 nm. For large spheres I need to adjust the  
>> cutt off
>> distance to accomidate them, which in turn stabalizes the water  
>> model, and
>> increases the solvation free energy. My work around is to have
>> two different
>> cuttoff distances one for water/water and one for water/solute. I
>> guess the
>> other option is to make a cavity using smaller spheres but one
>> sphere seems
>> simpler. Do you have any other suggestons?
>>
>> Thanks
>>
>> Ilya
>>
>>
>> -----Original Message-----
>> From: gmx-users-admin at gromacs.org  
>> [mailto:gmx-users-admin at gromacs.org]On
>> Behalf Of Eric Jakobsson
>> Sent: Tuesday, December 30, 2003 6:41 AM
>> To: gmx-users at gromacs.org
>> Subject: RE: [gmx-users] cutt offs
>>
>>
>> I apologize if I seemed abrupt---I was reacting to another list-serve  
>> that
>> I am on where there are lengthy debates that drown out the  
>> information.
>>
>> But think for a moment of the consequences of having a longer Coulomb
>> cutoff for ion-water than for water-water interactions, as you
>> suggested.  What you will do in that circumstance is overweigh the  
>> degree
>> to which the ion polarizes the water around it, leading to
>> systematic error
>> in, for example, ion diffusion constant and solvation energy inferred  
>> from
>> the calculation.
>>
>> Eric
>>
>> At 07:37 PM 12/29/2003 -0800, you wrote:
>>> The reason I was asking was not to debate the subject. I am growing  
>>> a LJ
>>> cavity in water. When the cavity gets really big beyond the standard  
>>> LJ
>>> cutoff I run into problems as one might imagine. I was looking
>> for a way to
>>> overcome this problem.
>>>
>>> By the way. A dipole-dipole interaction falls of faster than a
>> chrage-charge
>>> or charge-dipole.
>>>
>>> Thanks for your help!!!!
>>>
>>> Ilya
>>>
>>>
>>> -----Original Message-----
>>> From: gmx-users-admin at gromacs.org  
>>> [mailto:gmx-users-admin at gromacs.org]On
>>> Behalf Of Eric Jakobsson
>>> Sent: Monday, December 29, 2003 4:01 PM
>>> To: gmx-users at gromacs.org
>>> Subject: RE: [gmx-users] cutt offs
>>>
>>>
>>> Absolutely not.
>>>
>>> Probably too big a gap in perception here to profitably continue  
>>> such a
>>> debate.
>>>
>>> At 01:20 PM 12/29/2003 -0800, you wrote:
>>>> Your example is extreme. What about the case of a single charge in
>>>> water. The water-water Coulomb cut off should be less than the  
>>>> charge
>>>> water Coulomb cutoff.
>>>>
>>>> Ilya
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: gmx-users-admin at gromacs.org  
>>>> [mailto:gmx-users-admin at gromacs.org]
>>>> On Behalf Of David van der Spoel
>>>> Sent: Monday, December 29, 2003 12:40 PM
>>>> To: gmx-users at gromacs.org
>>>> Subject: RE: [gmx-users] cutt offs
>>>>
>>>> On Mon, 29 Dec 2003, Ilya Chorny wrote:
>>>>
>>>>> Its not obvious to me why the thermodynamics would get
>> screwed up. Its
>>>>> intuitively the same as having different cut offs for LJ vs Coul.
>>>> That is an approximation, and since LJ potential goes to zero  
>>>> faster it
>>>> can be justified (although that does not mean it is correct).
>>>> Treating different parts of the system with different
>>>> cut-off is worse. Let's say we divided a 6x6x6 nm system in two  
>>>> pieces,
>>>> that with X coordinate < 3 nm and that with X > 3 nm. Now if we use  
>>>> a
>>>> different cut-off for the first half of the system than for the  
>>>> other
>>>> half, we create artifacts on the border between the two, and what's
>>>> more,
>>>> I suspect that for such a system in "equilibrium" the chemical
>> potential
>>>>
>>>> is not the same in both halves. It will hence be impossible to  
>>>> define
>>>> what
>>>> kind of ensemble is modeled. Treating cut-offs differently for the
>>>> protein
>>>> and water is the same kind of division, comparable in nature to
>>>> simulations in implicit solvent.
>>>>
>>>>>
>>>>>> You would not want to do that anyway--it would really put you in
>>>>>> thermodynamic neverland.
>>>>> I agree, but IIRC this is what Amber does quite frequently,
>> no cut-off
>>>>> within the protein, and short cut-off for protein-water and
>> water-water
>>>>
>>>>> (e.g. the 1 us folding sim of Duan and Kollman).
>>>>
>>>> And to come back to that simulation, they also determined
>> solvation free
>>>>
>>>> energies from that, but from just the protein coordinates,  
>>>> dismiising
>>>> all the
>>>> solvent.
>>>>
>>>> Just my (possibly biased) opinion...
>>>>
>>>> --
>>>> David.
>>>
>>> _____________________________________________________________________ 
>>> ___
>>>> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
>>>> phone:  46 18 471 4205          fax: 46 18 511 755
>>>> spoel at xray.bmc.uu.se    spoel at gromacs.org
>> http://xray.bmc.uu.se/~spoel
>>>
>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
>>> +++
>>>>
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>>>
>>> ---------------------------------
>>> Eric Jakobsson, Ph.D.
>>> Professor, Department of Molecular and Integrative Physiology, and of
>>> Biochemistry
>>> Senior Research Scientist, National Center for Supercomputing
>> Applications
>>> Professor, Beckman Institute for Advanced Science and Technology
>>> 4021 Beckman Institute, mc251
>>> 405 N. Mathews Avenue
>>> University of Illinois, Urbana, IL 61801
>>> ph. 217-244-2896       fax 217-244-2909
>>>
>>> (Currently on leave to NIH to serve as Director of Center for
>>> Bioinformatics and Computational Biology at the National Institute of
>>> General Medical Sciences and Chair of the NIH Biomedical Information
>>> Science and Technology Initiative Consortium.  Usual schedule is
>> four days
>>> a week at NIH and three days a week at Illlinois.)
>>>
>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list
>>> gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list
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>>
>> ---------------------------------
>> Eric Jakobsson, Ph.D.
>> Professor, Department of Molecular and Integrative Physiology, and of
>> Biochemistry
>> Senior Research Scientist, National Center for Supercomputing  
>> Applications
>> Professor, Beckman Institute for Advanced Science and Technology
>> 4021 Beckman Institute, mc251
>> 405 N. Mathews Avenue
>> University of Illinois, Urbana, IL 61801
>> ph. 217-244-2896       fax 217-244-2909
>>
>> (Currently on leave to NIH to serve as Director of Center for
>> Bioinformatics and Computational Biology at the National Institute of
>> General Medical Sciences and Chair of the NIH Biomedical Information
>> Science and Technology Initiative Consortium.  Usual schedule is four  
>> days
>> a week at NIH and three days a week at Illlinois.)
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>>
>>
>> _______________________________________________
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>>
>
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