Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

it work together with the IMPI. I don't want to install openmpi as just a user also (did it a long time ago as root, not in limited space). Thanks again! On Fri, Nov 8, 2013 at 9:21 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade johanne

Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

Did it a few days ago. Not so much of a problem here. But I compiled everything, including fftw, with it. The only error I got was that I should turn off the separable compilation, and that the user must be in the group video. My settings are (yes, I know it should go better with openmp, but

Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

Really? An what about gcc+mpi? should I expect any improvement? On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham mark.j.abra...@gmail.comwrote: You will do much better with gcc+openmp than icc-openmp! Mark On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.com wrote: Did

Re: [gmx-users] GROMACS with GPU

Hi! If I may ask, but what is the gromacs version that is planned on the roadmap to begin to work with the newer version of openmm? Specially interested due to ATI support Regards Jones On Thu, Aug 18, 2011 at 10:01 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: Hi, Gromacs 4.5.x works only

Re: [gmx-users] gmxtest

Hi all. Sorry for waking up this subject again. But it rise a question for me: Is gmx 4 or gmx 3.3 that has a bug so? And, what is the bug concerned exactly? Buckingham interaction, 1-4 interactions, or buckingham 1-4 interactions? Thanks a lot in advance, Sincerally yours, Jones On Wed,

[gmx-users] TestBed in MPI not working

Hi everyone. Well, lets go straight to the point: last time I've installed gromacs, it was still 3.3.x and there was no testbed available yet. I've done some tests of my own and everything gone fine. I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They weem to work pretty well

Re: [gmx-users] TestBed in MPI not working

that I'm really thinking IF I'll make it available in the new cluster. :P This has to be any sort of pretty stupid mistake so. But I'm clueless this time. :( Any ideas? Thanks a lot in advance! :) Jones On Mon, May 11, 2009 at 7:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jones de Andrade

Re: [gmx-users] TestBed in MPI not working

Hi Justin This has been discussed several times on the list. The -np flag is no longer necessary with grompp. You don't get an mdrun.out because the .tpr file is likely never created, since grompp fails. Yes, I know that and that is what I would have expected. But what I'm running is the

Re: [gmx-users] TestBed in MPI not working

wrote: Jones de Andrade wrote: Hi Justin This has been discussed several times on the list. The -np flag is no longer necessary with grompp. You don't get an mdrun.out because the .tpr file is likely never created, since grompp fails. Yes, I know that and that is what I would

Re: [gmx-users] TestBed in MPI not working

I go straight to recompilation, despite there is no reason for failure here? Thanks a lot! Jones On Mon, May 11, 2009 at 10:42 PM, Jones de Andrade johanne...@gmail.comwrote: Hi Justin. Well, bothering again. Good and bad news. The good news: I found a strange work-around for my problems

Re: [gmx-users] TestBed in MPI not working

Hi Justin. On Mon, May 11, 2009 at 11:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: All of the above can be fixed by changing the appropriate .mdp option. Yes, I agree. I'll try that. Probably that's what will solve that problem. If that's ok, I'll send to the site a revised version of the

Re: [gmx-users] Re: Nehalem

One point here is the fact that on specfp gromacs is NOT compiled with the assembly parts. Those come from fortran. Performance hit, in different ways from different architectures and compilers due to this. ;) On Fri, Feb 13, 2009 at 10:04 AM, sobereva sobju...@yahoo.com.cn wrote: Hi,

Re: [gmx-users] Martini + other force field

Am I wrong, or are you considering some kind of MSCG (which is not into gromacs at least in a standard, straight forward out of the box way)? That's nice, would be really interesting to implement, would take long time and is still a relativelly open-field with lot to be still explored. I think we

Re: [gmx-users] ionic liquid

Hi naimah. Sorry for the late replay, but I was travelling. What kind of ionic liquids are you interested in? If they are the dialkyl-immidazolium ones, I'm doing simulations on these systems for quite some time now (please look at these references: Journal of Physical Chemistry B, v. 112, p.

Re: [gmx-users] nature of gromacs / gcc-4.x problem

Just addin my drop here: Just did the same, both single and double precision, not parallel anyway. What I get is the following: *aurora down/gmxtest 41%* ./gmxtest.pl all All 16 simple tests PASSED FAILED. Check files in dec+water 1 out of 14 complex tests FAILED All 63 kernel tests PASSED All

[gmx-users] old patch for slow networks

Hi all. I'm writing this message to ask a simple and direct question: the available patch of gmx3 for slow networks, that includes the ordered-all-to-all procedures, seems fo be indicated for version 3.1. It's still necessary for slow networks using gmx3.3? Thanks a lot in advance...

Re: [gmx-users] Dummies usage doubts

was completelly wrong. Thanks a lot in advance, Sincerally yours Jones On 10/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. Well, I'm having a bit of trouble here because the work has decided to go in the direction of something I've never used before

Re: [gmx-users] Dummies usage doubts

Hi Prof. David. What details do you mean? Actual topology files are attached. Anything else? Thanks a lot in advance! Sincerally yours, Jones On 10/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Thanks Prof. David. I've done all that now, but at the moment

Re: [gmx-users] Dummies usage doubts

it is. Can you provide me some clue on this? I'll run a single molecule now. Thanks a lot in advance, Sincerally yours, Jones On 10/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Prof. David. What details do you mean? Actual topology files are attached. Anything

Re: [gmx-users] Dummies usage doubts

with many molecules or even single molecule MD, God? Thanks a lot everybody in advance, Sincerally yours, Jones On 10/11/07, Jones de Andrade [EMAIL PROTECTED] wrote: Hi Prof. David. Yes, it a self created topology. This one is based on another self created topology that runs perfectly

Re: [gmx-users] Dummies usage doubts

, though. Anyway, thanks a lot everybody for all help! :) Sincerally yours, Jones On 10/11/07, Jones de Andrade [EMAIL PROTECTED] wrote: Hi all. Just informing, I tried a single molecule, and the topology with all dummies minimize (despite taking loads of steps bfgs steps). The interesting

Re: [gmx-users] Reading XTC files from fortran90

Hi all. First of all, I would really want want to apologize if I somehow missunderstood any previous message from anyone, and made myself a bit annoying because of this fact. Second, I would like to say thanks again to eferybody for all help in these matters. On 10/1/07, Tsjerk Wassenaar [EMAIL

Re: [gmx-users] Reading XTC files from fortran90

in PBC. The lattice vectors are all there is, and these are stored in the .xtc file (as you already know). Cheers, Tsjerk On 9/30/07, Jones de Andrade [EMAIL PROTECTED] wrote: Hi Bert. Thanks a lot for the help. I've found the mistakes, one programming minor issue and a compiler

Re: [gmx-users] Reading XTC files from fortran90

! Sincerally yours, Jones On 9/30/07, David van der Spoel [EMAIL PROTECTED] wrote: Mark Abraham wrote: Jones de Andrade wrote: Hi Tsjerk. Thanks for the prompt answer. Good idea, I can take the atom names from a .gro file, nad, probably some strange algorithm can also get the number

Re: [gmx-users] Reading XTC files from fortran90

Hi Mark. Wait a second, you mean that editconf would allow me to have both charges and masses on a .pdb file directly from command line (having other matters asking for my presence absolutelly now, so please forgive me if this message becomes somehow strange) So, I would have atom names, number

Re: [gmx-users] Reading XTC files from fortran90

Hi Bert. Thank you for the prompt answer. Just did as instructed, but got the following: CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90 -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c IPO link: can not find -lxrdf ifort: error: problem during multi-file optimization compilation

Re: [gmx-users] Reading XTC files from fortran90

, Jones de Andrade wrote: Hi Bert. Thank you for the prompt answer. Just did as instructed, but got the following: CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90 -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c IPO link: can not find -lxrdf well, apparently

[gmx-users] Reading XTC files from fortran90

Hi all. I'm writing this beucase I'm having terrible problems in trying to deal with gromacs trajectory files with my own programs, originally written on fortran90. The codes themselves are enoughly big to make it out of question to try to translate them. What leads to some sort of mixed

[gmx-users] fortran xtc reading problem?

Hi. I'm trying to read some .xtc file trajectory files throw my fortran codes, following the guidelines from http://xray.bmc.uu.se/~spoel/md/online/xtc.html Also later found this html file on the gromacs directory here. ;) Anyway, I got stuck at some really strange point: I'm basically not

[gmx-users] a future gmx 4.0 doubt

forgive me again for my intrusion. ;) Sincerally yours, Jones On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Mark. Haven't got exactly what you said. So let me rephrase myself: The CF4 molecule doesn't have dihedrals nor intramolecular LJ

Re: [gmx-users] New single thread performance numbers

Hi Erik. Still under NDA? Haven't it been lift last sunday? Anyway: I don't know exactly the terms of the NDA, So if you can't answer me the following question, please say no, I can't answer. I'm in touch with people having some compability issues with their Barcellonas and MBs, so could you

Re: [gmx-users] How to Install GMX V3.3.1 with Intel fortran compiler?

Hi. Yes, but that is the gcc solution. No prblem with those, except for giving away the challenge to make it work with intel compilers. Basically: I couldn't find a way much better. The way I trid in the time I tried, included compilation of the loops and only the loops using gcc to make the

Re: [gmx-users] Ionic liquids

Hi. I would not agree with the fact that the approach isn't good. The dialkylimidazolium cation class has a lot of interest on it, which leaded to the development of force field for them rather than others. It doesn't mean that there isn't force field for the [EtNH3]+ [NO3]- IL, but means that

[gmx-users] PME or SPME?

Hi all. Well, I have some kind of a didatic doubt: Ok, from what I can understand up to now, PME uses lagrande interpolation for the genaration of the grid, while SPME uses cardinal B-splines to do so. Is it correct? And if, so, gromacs implements PME or SPME (the manual states PME, but also

Re: [gmx-users] Ionic liquid parameters

Hi people. Well, this thread is going to become an independet list for ILs. We have developed a force field for a small set of cations and anions of ILs, few year ago, based on AMBER. At the moment, we are (slowly) finalizing publications on the extension of those for new sets of anions, all

[gmx-users] how to remove an energy contribution in gromacs?

Hi all. Well, I'm trying to calculate an E energy from my simulations, where E here stands only for the sum of *intermolecular* vdw and coulombic terms, and LJ(1-4) and coul(1-4). This means that I should find a way to exclude any 1-5, 1-6, 1-7 and so on contributions for coulombic and vdw

Re: [gmx-users] how to remove an energy contribution in gromacs?

. :( Any other thoughts? Thanks a lot, Jones On 8/6/07, Mark Abraham [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. Well, I'm trying to calculate an E energy from my simulations, where E here stands only for the sum of *intermolecular* vdw and coulombic terms, and LJ(1-4

Re: [gmx-users] how to remove an energy contribution in gromacs?

Hi both. @ Mark: thanks mark. Have to admit that I haven't thought about the exclusions possibility. Specially because I was looking for a simple way of doing it without removing the dynamics related to these forces from the simulation itself. So, changing the nexcl looked a bit easier to do. @

Re: [gmx-users] how to remove an energy contribution in gromacs?

frequency mdrun -rerun will update them every 5/10*10ps ... XAvier From: Jones de Andrade [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] how to remove an energy

[gmx-users] mdrun -rerun + runedr: combo problem?

Hi all. I think I'm having a really strange problem: Well, I have some simulations being performed, and wanted to remove from the bigger molecules any vdw or coulombic intramolecular interaction longer than 1-4. So, from 1-5 included forward, I would like to remove from the energetic

[gmx-users] More dihedral doubts

Hi all again. Sorry for bothering all you with this dihedrals subject. Well, I'm trying this in my .itp file: ** [ dihedraltypes ] ; i j k l functphi (degree) cp (kJ/mol.rad^2) mult(n) CTCTNT

Re: [gmx-users] Help with RB dihedrals implementation

CT-CT will be defined by the potential described in the fourth line, correct? If anyone could confirm or deny it for me that would be really helpfull. Thanks a lot in advance for everything. Jones On 7/27/07, Mark Abraham [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Mark. Thanks

[gmx-users] dihedral doubts, again

Hi all. Well, I'm having a few problems in implementing an opls-like dihedral potential, what mean, a serie of different periodic dihedral potentials. After much problem with the RB potential conversion, Ifound on the net that the 3.3.1 version of gromacs allows me to use sum of different

Re: [gmx-users] Help with RB dihedrals implementation

Hi Mark. Thanks a lot. I'm already trying to find some clue in the manual. Anyway, what sort of extra information could be usefull? Thanks a lot again! ;) Jones On 7/26/07, Mark Abraham [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. I'm trying to implement a samll RB

[gmx-users] Help with RB dihedrals implementation

Hi all. I'm trying to implement a samll RB-potential for some molecules I'm working with. I choosen to go following the files from opls-aa force field included with gromacs. Unfortunatelly, I get this error: No default Proper Dih. types, using zeroes Which is quite strange, as the error

[gmx-users] Buckingham Potential Doubt.

Hi all. I was just wondering, and I even think this is a stupid question: As well as there are the Lorentz-Berthelot combination rules (among others) for the sigma and epsilon from Lennard-Jones parameters of different atom types, how can the parameters from Buckingham potential of different

Re: [gmx-users] intermolecular energy

Hi Mark. Haven't got exactly what you said. So let me rephrase myself: The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic contributions. What kind of contribution am I missing that makes potential energy minus bond stretching minus angle bending *different* from Lj +

Re: [gmx-users] intermolecular energy

missing? Thanks a lot! Jones On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Mark. Haven't got exactly what you said. So let me rephrase myself: The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic contributions. What kind

Re: [gmx-users] intermolecular energy

can be lacking where? Thanks a lot in advance, Sincerally yours, Jones On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi David! Ha, so there is something extra? Thanks a lot :) I knew I was forgeting something. So how should I deal with it? I mean

Re: [gmx-users] intermolecular energy

, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi David! Ha, so there is something extra? Thanks a lot :) I knew I was forgeting something. So how should I deal with it? I mean, what are the contibutions that are inside the Potential option of g_energy? Does

Re: [gmx-users] intermolecular energy

= 12041979 On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. First, I would like to apologize for the previous message. Maybe I've been too harsh? Sorry for that. Second, I would like to list all the energetic contributions for one (same system

Re: [gmx-users] intermolecular energy

: Jones de Andrade wrote: Hi David. Well, as long as I can remember, I pushed the last gromacs sources at time (3.3.1) and just installed it. Anyway, mdrun tells me it is 3.3 and g_energy says it is 3.2.1 (in the run headers). I expected this to be normal, or could I have run in some kind

[gmx-users] BFGS in NMA calculations?

Hi! I was just wondering: am I completelly wrong, or gromacs uses the BFGS hessian approximation in order to do normal mode analysis, rather than the real and painfull to analitically second derive potentials hessian? I'm wondering also if this approximation is as good for NMA as it is for

Re: [gmx-users] Polarizability

de Andrade wrote: Hi list. Well, a few days ago I've written a message concerning the future implementations that could be expected min gromacs 4 when it's released. Unfortunatelly, the thread hasn't gone any further. lots of plans, but no promises. we really don't want to raise any

[gmx-users] Polarizability

Hi list. Well, a few days ago I've written a message concerning the future implementations that could be expected min gromacs 4 when it's released. Unfortunatelly, the thread hasn't gone any further. So, I would like to know if there is somone in this list who ever tried to modify gromacs

[gmx-users] gromacs future development guidelines?

Hi Al.. Well, first of all sorry if this message becomes a bit out of the scope of the list. Since I've heard a lot of time ago somewhere in here that the gromacs 4.0was in development, today I remembered that and decided to ask google to give this a try. I basically found this 2 documents

[gmx-users] Compressibility issue - real concern

Hi all. Well, I'm having a great problem in some NpT simulations I'm running here, which leaded me to some concerns. Let me try to explain the situation: Ok, I know: everywhere, including this list, amber list and any computational chemistry list informs that the compressibility of the liquid

Re: [gmx-users] Compressibility issue - real concern

to this question, and this is how this ended: *** Hi, ** ** Just use the water value for any liquid system (5e-5 or so). ** ** As the manual explains, it only affects the coupling time, not the ** equilibrium pressure. ** ** Cheers, ** ** Erik ** On May 3, 2006, at 8:54 PM, Jones de Andrade wrote: ** ** Hi

Re: [gmx-users] Compressibility issue - real concern

? Thanks a lot in advance! Sincerally yours, Jones On 5/3/07, Erik Lindahl [EMAIL PROTECTED] wrote: Hi, On May 3, 2007, at 12:37 PM, Jones de Andrade wrote: Hi Berk! Thanks for your so fast answer! I'll try to look for a different tau_p. I would really feel 4 ps a too high value, even

Re: [gmx-users] using fortran for xtc files

Hi all! About the same subject... Does anybody ever tried to read the topology files from gromacs within fortran? I would accept some C routines for this if necessary... :) Thanks a lot, Jones On 3/24/07, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Gurpreet, Try to get your hands on the

Re: [gmx-users] using fortran for xtc files

ones should I look at? Sorry for not making myself clear in the previous message. Thanks a lot in advance, Jones On 3/24/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all! About the same subject... Does anybody ever tried to read the topology files from gromacs

[gmx-users] Problems in C8 and C9 chains equilibration

Hi everybody. I would like to ask one question, basically about equilibration of long and flexible alkyl chains. I'm having terrible problems in equilibrating C8 and C9 chains. I've already expanded a lot the box size, but I always fall into segmentation faults. Also tried smaller time steps

Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)

Hi Erik. Well, I don't even use the [pairtypes] section in my files. Only use the [pairs] one, in the way explained before. This means, so, that it should not have any problem, and reduce independently the LJ potentials by a factor of 0.5, and coulombic interations by a factor of 0.8333,

Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)

not have any problem, and reduce independently the 1 - 4 LJ potentials by a factor of 0.5, and 1 - 4 coulombic interations by a factor of 0.8333, correct? Tnaks a lot in advance, Sincerally yours, Jones On 2/13/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Erik

FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)

Hi guys. Well, I'm not exactly trying t reopen an old discussion. I'm trying to see a different aspect from it, as the subject indicates. Since the message reproduced below is the last of the fudges questions, I'm worried about the fact of the fudgeLJ meaning nothing for the simulation. First,

[gmx-users] Re: parallel in duals?

: Jones de Andrade wrote: Ok, I know this subject have been discussed in the past. But I started to wander if the basic conclusion (do not use in parallel, you should rather use on job for each core) is still up, and if it is, if there is any hope of change in a foresight future, as well on how much

[gmx-users] Re: parallel in duals?

.). So, since I'm locked in a socket, I'm wandering what's better: the highest clock possible, or less clock with two cores? Thanks a lot... Jones On 8/1/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi David. Well, it wasn't me who did the test. :) My problem

[gmx-users] parallel in duals?

Ok, I know this subject have been discussed in the past. But I started to wander if the basic conclusion (do not use in parallel, you should rather use on job for each core) is still up, and if it is, if there is any hope of change in a foresight future, as well on how much real loss is observed

[gmx-users] Grompp Fudge Problems?

Hi all!.I was trying to simulate a complex cation in MeCN solution and this called my attention: grompp gives me: Generating 1-4 interactions: fudge = 0.5. It's not wrong, since I put this fudge for the VdW interactions, BUT I also placed a different fudge for the intramolecular coulombic

[gmx-users] Grompp errors?

Hi all!. I was trying to simulate a complex cation in MeCN solution and I got 2 strange warnings to me: processing topology... WARNING 1 [file ff_emi.itp, line 7]: Overriding atomtype CT WARNING 2 [file ff_emi.itp, line 11]: Overriding atomtype H1 But I did found that strange because, as you

Re: [gmx-users] intel compiler + amd64: help needed.

Hi all. Of course I want SSE enabled. There is no sense in benching it against different compilers if in one you enable the speed and on the other, and in the other you remove almost every optimization. That's why in the last message I've sent the eror I'm getting in the compilation:

Re: [gmx-users] intel compiler + amd64: help needed.

Ok, I think I got it. Compiled. ;) About a thousand tricks. I'll publish a tutorial later. But, basically: 1 - Change all invsrt calls to gmx_inv-sqrt (57 entries, 12 files); 2 - Edit the Makefile.in in the nb_kernels directories, changing the line LTCCASCOMPILE = $(LIBTOOL) --mode=compile

Re: [gmx-users] intel compiler + amd64: help needed.

Hi all!. First, sorry for the delay in getting in touch again. Bureaucracy. :P Second, thanks a lot for everybody for advising on this subject. It's helping me a lot to solve this! :) Anyway, here is where I'm now: Erik: I'm sure about the flags. Not using the ones for SSE3, despite my

Re: [gmx-users] intel compiler + amd64: help needed.

Hi all. On 6/1/06, David van der Spoel [EMAIL PROTECTED] wrote: Trying withou the -ipo flag now. It still yelds the same weird warning (warning #147: declaration is incompatible with double invsqrt(double) (declared at line 565 of /usr/local/intel/include/math.h)rename all gromacs invsqrt calls

Re: [gmx-users] intel compiler + amd64: help needed.

Hi all. :) Last message today. It seems that I succeded in switching all invsqrt functins to a new gmx_invsqrt. Just 57 in the 12 files below: *** include/vec.h src/mdlib/csettle.c src/mdlib/vsite.c src/mdlib/clincs.c

Re: [gmx-users] intel compiler + amd64: help needed.

Hi David. First, thanks for your time. ;) Unfortunatelly, it seems that the simple flag it is not quite enough still... :( If it was not a well known fact that intel compiler yelds you some extra performance for gromacs, and if I would not want to try to make QM/MM of gromacs+cpmd (and, in this

Re: [gmx-users] intel compiler + amd64: help needed.

Hi David. Thanks a lot. But almost there. first, coulsave is already n int type variable: int vdwsave,coulsave,read_from_mem,write_to_mem; (line 294) So, the change from: mknb_func.coul=coulsave; mknb_func.vdw=vdwsave; To: mknb_func.coul=(int)coulsave; mknb_func.vdw=(int)vdwsave; Was

Re: [gmx-users] intel compiler + amd64: help needed.

, substitute it by the old Mkefile in the mknb directory and then make? (Trying this now) Thanks in advance for everything. JonesOn 5/31/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. Program received signal SIGSEGV, Segmentation fault. 0x2b15a88c in __find_specmb

Re: [gmx-users] intel compiler + amd64: help needed.

Hi all. First of all, thanks everybody for the help. ;) Yang, I know, I know. I should keep to the GNU. But lets say that I get addicted to the intel compiler on a cpmd winter school, when it appeared in front of me as the only freely available for both amd and intel cpus fortran90 compiler.

[gmx-users] Re: Benching against different compilers - Help needed

Hi again. Well, here we go: On 4/30/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Up to now, I could finally compile it with Portland, in both single and double precision version. But, on the other hand, while the single precision works properly, the double

[gmx-users] Compressibility in NpT: What value to input?

Hi all. Ok, this may sound like a stupid question, since the equations of the barostats clearly states the compressibility constant in it. But, in other programas I used to do NpT (usually with Nosè-Hoover) simulations, like DL_Poly and MDynaMix, I never had to input this parameter. Only

Re: [gmx-users] Compressibility in NpT: What value to input?

for any liquid system (5e-5 or so).As the manual explains, it only affects the coupling time, not theequilibrium pressure.Cheers,ErikOn May 3, 2006, at 8:54 PM, Jones de Andrade wrote: Hi all. Ok, this may sound like a stupid question, since the equations of the barostats clearly states

Re: [gmx-users] Re: Mix solvent

Hi! Ops! I forgot to paste the web address! :P Here it goes: http://www.ime.unicamp.br/~martinez/packmol/ And, yes: It's GPL too. ;) JonesOn 4/27/06, Mark Abraham [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi. Well, I don't know if the list allows the indication of out-gromacs programs

[gmx-users] Benching against different compilers - Help needed

Hi all. Well, some time ago I decided to bench gromacs on AMD64 machines compiled with different compilers (both single and double precision, both internal and external blas and lapack, just FFTw 3 for fourier) in order to see which one performs better. To time, I have available GCC, PGI and

Re: [gmx-users] Installation Error on an Athlon64 with Intel Compiler

Hi again! Well, still having problems: /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_interactions.o mknb_interactions.c /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -o mknb mknb.o mknb_metacode.o mknb_common.o mknb_declarations.o

Re: [gmx-users] FFTW installation error: cannot compile asimpleFortran program

Hi all! Ok, I did not acquired to compile gromacs with intel yet, but now I'm also facing problems with PGI compilers (which also has the extra problem of needin to be redownloaded soon). Just in case someone asks: I'm trying to benchmark gromacs in A64s with different compilers. ;) Well, PGI

[gmx-users] Re: PGI compilation error: --rpath problem?

precision then. :( Any idea of what to do now? Anyway, thanks a lot for everything. Jones On 4/24/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Ok, thanks a lot. adding the wthout x and motif stuff in configure, plus the corrections for gmx_sgangle.c found

Re: [gmx-users] PGI compilation error: --rpath problem?

and Unfold (Macbeth, Act 3, Scene 6, William Shakespeare). Finally, it behaves like that while using the PGI compilers. It works properly with GCC. Any ideas of where to go now? :( Thanks for everything. JonesOn 4/24/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Ok, thanks