Re: [gmx-users] Post simulation energy calculation of Ligand - Protein complex
On 17/03/11, Rahul ShubhraMandal rahul.man...@igib.in wrote: Hi, I want to calculate the binding energy of ligand-protein complex after simulation. I am running 10ns simulation, please help me out in this regards. Thanks. Please start by finding some literature that does something similar to what you would like to do. Then think and read about how that might be done in GROMACS. Then, please ask a more focussed question :-) Mark -- 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
AW: [gmx-users] lipopeptide problem
If you want the lipid connected to the amino acid, i think it would be a good idea to add a new residue type to aminoacids.rtp which contains both, your lipid and the amino acid its connected to. You can start from the rtp entry of the amino acid and add the lipid parameters. After doing that, you can use pdb2gmx to build the topology for the whole system even without any need to adjust the .top afterwards. The link you gave is the right place to get a route for this intent. Good luck. Felix Von: gmx-users-boun...@gromacs.org im Auftrag von Emine Deniz Tekin Gesendet: Mi 16.03.2011 22:53 An: gmx-users@gromacs.org Betreff: [gmx-users] lipopeptide problem Hi GROMACS Users, I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I simulated a peptide before but this is the first time I am trying to combine a lipid with a peptide (to get a lipo-peptide). I would be really happy if you could help me out with the following question I am tring to create a louroic acid connected to and an 8-redidue peptide. To create residues, I used ARGUSLAB . For the louric acid I used BERGER lipid parameters. Then, as described in KALP-15 in DPPC tutorial, I combined ffbonded.itp and ffnonbonded.itp with lipid.itp. I also adjusted the topol.top files as described in the manual. But this procedure did not yet give me an attached louric acid and peptide. I still have to play with the aminoacids.hdb, aminoacids.rtp, residuetypes.dat, atomtypes.atp, and specbond.dat files. I would appreciate if you could let me know how to modify these files, especially the aminoacids.hdb file. I tried several things but it not work. Note that, I applied the suggestions in http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, but it was not sufficient. Best regards Deniz -- 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
Re: [gmx-users] Energy calculation
Hi, Every charge group must be a subset of an energy group or fully disjoint from it. Does it mean that I could not set up the HBD and HBA in the ligand at the same time, but the HBD in ligand and HBA in lipid bilayer could be calculate? or Each atoms in the ligand must belong to the disjointed subset? For the guess 2, I try to modify the .ndx file and add the nHB (non-HB-system). The atoms in nHB are excluded from HBA and HBD in the ligand. [ nHB ] 17366 17368 17369 17370 17371 17372 17373 17374 17376 17377 17378 17379 17380 17383 17386 17389 17390 17391 17392 17393 17394 17395 17396 17397 17398 17399 17401 17402 17403 17405 17406 17407 17408 17409 17410 17411 17413 17414 17415 17416 17417 17420 17423 17426 17427 17428 17429 17430 17431 17432 17433 17434 17435 17436 17438 17439 17440 17442 17443 17444 17445 17446 17447 17448 17450 17451 17452 17453 17454 17457 17460 17463 17464 17465 17466 17467 17468 17469 17470 17471 17472 17473 17475 17476 17477 17479 17480 17481 17482 17483 17484 17485 17487 17488 17489 17490 17491 17494 17497 17500 17501 17502 17503 17504 17505 17506 17507 17508 17509 17510 17512 17513 17514 17516 17517 17518 17519 17520 17521 17522 17524 17525 17526 17527 17528 17531 17534 17537 17538 17539 17540 17541 17542 17543 17544 17545 17546 17547 17549 17550 [ HBD ] 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 [ HBA ] 17367 17375 17381 17384 17387 17388 17400 17404 17412 17418 17421 17424 17425 17437 17441 17449 17455 17458 17461 17462 17474 17478 17486 17492 17495 17498 17499 17511 17515 17523 17529 17532 17535 17536 17548 But the error msg. is alike. Fatal error: atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in different energy groups Do you have any methods for calculating the HB energy in the intramolecules? Thanks for your any comments. Best, Chia-yun Chang 2011/3/16 Mark Abraham mark.abra...@anu.edu.au On 16/03/11, *C.Y. Chang * chiayun.ch...@gmail.com wrote: Hi, I try to calculate the Hbond in the ligand and remove the duplicate atoms in the .ndx file dumped from g_hbond. This is the contents in the .ndx file. [ HBD ] 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 [ HBA ] 17367 17375 17381 17384 17387 17388 17400 17404 17412 17418 17421 17424 17425 17437 17441 17449 17455 17458 17461 17462 17474 17478 17486 17492 17495 17498 17499 17511 17515 17523 17529 17532 17535 17536 17548 And then, I perfrom the grompp. It shows the error msg. Fatal error: atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in different energy groups How should I deal with the problem? Redefine charge or energy groups as appropriate for whatever you're trying to do. Non-bonded interactions are calculated by looping over atom-atom interactions grouped by charge group and then by energy group. Every charge group must be a subset of an energy group or fully disjoint from it. On the other side, I read the information in the web page ( http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html) I remove the lines in the [bonds] region in .top files. But I still get these terms 1 Angle2 G96Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 Improper-Dih.6 LJ-147 Coulomb-14 8 LJ-(SR) 9 Disper.-corr. 10 Coulomb-(SR)11 Coul.-recip.12 Position-Rest. 13 Potential 14 Kinetic-En. 15 Total-Energy16 Temperature 17 Pres.-DC18 Pressure19 Constr.-rmsd20 Box-X 21 Box-Y 22 Box-Z 23 Volume 24 Density 25 pV 26 Enthalpy27 Vir-XX 28 Vir-XY 29 Vir-XZ 30 Vir-YX 31 Vir-YY 32 Vir-YZ 33 Vir-ZX 34 Vir-ZY 35 Vir-ZZ 36 Pres-XX 37 Pres-XY 38 Pres-XZ 39 Pres-YX 40 Pres-YY 41 Pres-YZ 42 Pres-ZX 43 Pres-ZY 44 Pres-ZZ 45 #Surf*SurfTen 46 Mu-X47 Mu-Y48 Mu-Z 49 Coul-SR:LIG-LIG 50 LJ-SR:LIG-LIG 51 Coul-14:LIG-LIG 52 LJ-14:LIG-LIG 53 Coul-SR:LIG-DPPC_SOL54 LJ-SR:LIG-DPPC_SOL 55 Coul-14:LIG-DPPC_SOL56 LJ-14:LIG-DPPC_SOL 57 Coul-SR:DPPC_SOL-DPPC_SOL 58 LJ-SR:DPPC_SOL-DPPC_SOL 59 Coul-14:DPPC_SOL-DPPC_SOL 60 LJ-14:DPPC_SOL-DPPC_SOL 61 T-DPPC 62 T-SOL 63 T-LIG 64 Lamb-DPPC 65 Lamb-SOL66 Lamb-LIG And I try to remove lines in [bonds], [pairs], [angles] and [ dihedrals ], but it is the same. Where is the wrong process? And how could I get the angle and dihedral energy in the
[gmx-users] Regarding editconf
I have some questions regarding editconf: 1)If we did'nt mentioned -box parameters,the *default vectors are 0 0 0*, why it is zero and what does it mean? 2)How to determine distance between the solute and the box, is it appropriate to take it 0.9 nm for a globular protein of 179 amino acids. After running editconf using the command *editconf -bt cubic -f 1.pdb -o 2.pdb -c -d 0.9* I got the following output: Read 3256 atoms Volume: 515.892 nm^3, corresponds to roughly 232100 electrons No velocities found system size : 4.217 4.721 4.631 (nm) diameter : 5.270 (nm) center : 1.974 2.562 0.035 (nm) box vectors : 7.602 7.602 10.309 (nm) box angles : 90.00 90.00 120.00 (degrees) box volume : 515.89 (nm^3) shift: 1.562 0.973 3.500 (nm) new center : 3.535 3.535 3.535 (nm) new box vectors : 7.070 7.070 7.070 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 353.45 (nm^3) I have some question regarding this output: 1)Why new box volume decreased?And what does it mean? 2)Why the new length of box vectors decreased?And what does it mean? 3)How gromacs assign vectors length?If not provided in the editconf command. 4)How gromacs place solvent inside the box(genbox) , I mean using which method and how gromacs determine the the number of solvent to be placed inside the box. --- *Regards,* Bipin Singh -- 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
[gmx-users] installation of gromacs
Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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
Re: [gmx-users] installation of gromacs
Hi Thomas, please send the complete config.log. After you try what I suggest bellow. I guess the environment variables for compilers and libs are not set correctly, not your fault, we'll check on the config file. #make sure your're usnig bash bash #export the regular variables export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib #also try this one export LD_LIBRARY_PATH=$HOME/local/fftw3/lib #and by now, remove the --enable-shared ./configure --prefix=$HOME/local/gromacs On Thu, Mar 17, 2011 at 10:44 AM, Thomas Koller koller-tho...@gmx.de wrote: Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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 -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. -- 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
Re: [gmx-users] installation of gromacs
On Thu, 2011-03-17 at 10:44 +0100, Thomas Koller wrote: Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? This means that the compiler does not work properly. I also encountered this error some time ago, but I can not remember, what the reason exactly was. However I would always go for the latest release and preferably fetch the release branch (check the website for a How To) Cheers, Flo Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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
Re: [gmx-users] Regarding editconf
On 17/03/11, bipin singh bipinel...@gmail.com wrote: I have some questions regarding editconf: 1)If we did'nt mentioned -box parameters,the default vectors are 0 0 0, why it is zero and what does it mean? It means no box is defined. 2)How to determine distance between the solute and the box, is it appropriate to take it 0.9 nm for a globular protein of 179 amino acids. After running editconf using the command editconf -bt cubic -f 1.pdb -o 2.pdb -c -d 0.9 At a minimum, you want no solvent atom to be able to see two images of your solute. So depending on your rcoulomb/rvdw/rlist regime, you are probably at the minimum that would be reasonable. If your globular protein expands at all, or can uncoil some loops, you might not have a sound model. I got the following output: Read 3256 atoms Volume: 515.892 nm^3, corresponds to roughly 232100 electrons No velocities found system size : 4.217 4.721 4.631 (nm) diameter : 5.270 (nm) center : 1.974 2.562 0.035 (nm) box vectors : 7.602 7.602 10.309 (nm) box angles : 90.00 90.00 120.00 (degrees) box volume : 515.89 (nm^3) shift : 1.562 0.973 3.500 (nm) new center : 3.535 3.535 3.535 (nm) new box vectors : 7.070 7.070 7.070 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 353.45 (nm^3) I have some question regarding this output: 1)Why new box volume decreased?And what does it mean? The old box was bigger. Have a look at the relevant part of your input file. 2)Why the new length of box vectors decreased?And what does it mean? You implicitly told it a cubic box size you wanted with the -d flag, i.e. the size of protein plus the margin of 0.9nm. Whether that's a decrease is not relevant. 3)How gromacs assign vectors length?If not provided in the editconf command. See above. 4)How gromacs place solvent inside the box(genbox) , I mean using which method and how gromacs determine the the number of solvent to be placed inside the box. See genbox -h. Mark -- 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
Re: [gmx-users] installation of gromacs
Hi Thomas, the error you see indeed suggests that something is messed up with your compiler. In your case however I think that is due to the CPPFLAGS and LDFLAGS you set. Those sometimes mess with the configure makros. Try export CPPFLAGS= export LDFLAGS= export LD_LIBRARY_PATH= to erase what you set previously (or open a fresh shell actually) And then try using the -with-fftw configure parameter instead. Best Tim On 3/17/11 10:44 AM, Thomas Koller wrote: Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? Regards, Thomas -- 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
[gmx-users] installation of gromacs
Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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
Re: [gmx-users] installation of gromacs
On 17/03/11, Thomas Koller koller-tho...@gmx.de wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float You've installed in /home/local/fftw3... - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib ... but told configure later to look in /home/local/fftw That doesn't work. Even when it does, it's likely that you'll still need to look at the last few hundred lines of config.log to actually diagnose the problem... Mark iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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 -- 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
Re: [gmx-users] installation of gromacs
You got this wrong export CPPFLAGS=-I/home/local/fftw/include export LDFLAGS=-L/home/local/fftw/lib replace by this export CPPFLAGS=-I$HOME/local/fftw/include export LDFLAGS=-L$HOME/local/fftw/lib On Thu, Mar 17, 2011 at 12:24 PM, Thomas Koller koller-tho...@gmx.de wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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 -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. -- 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
Re: [gmx-users] installation of gromacs
Thomas Koller wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? Your CPPFLAGS and LDFLAGS are wrong. If you installed FFTW in $HOME/local/fftw3, then the appropriate settings are CPPFLAGS=-I$HOME/local/fftw3/include LDFLAGS=-L$HOME/local/fftw3/lib Note that your original error is related to the C compiler, not FFTW. You've been prompted several times to post relevant lines in config.log, but you haven't, so please do, otherwise you (and everyone on the list) will keep hacking away with no result. What C compiler is installed on your system? Where is it installed? Is it in your PATH? -Justin I wish I can have access soon. :( Thomas -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
On 17/03/11, Diego Enry diego.e...@gmail.com wrote: You got this wrong export CPPFLAGS=-I/home/local/fftw/include export LDFLAGS=-L/home/local/fftw/lib replace by this export CPPFLAGS=-I$HOME/local/fftw/include export LDFLAGS=-L$HOME/local/fftw/lib This is immaterial if Thomas installed to $HOME/local/fftw3 Mark On Thu, Mar 17, 2011 at 12:24 PM, Thomas Koller koller-tho...@gmx.de wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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 -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. -- 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 -- 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
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 123
I managed it now. Thanks for all your help. Thomas Original-Nachricht Datum: Thu, 17 Mar 2011 14:26:46 +0100 (CET) Von: gmx-users-requ...@gromacs.org An: gmx-users@gromacs.org Betreff: gmx-users Digest, Vol 83, Issue 123 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. installation of gromacs (Thomas Koller) 2. Re: installation of gromacs (Mark Abraham) 3. Re: installation of gromacs (Diego Enry) 4. Re: installation of gromacs (Justin A. Lemkul) 5. Re: installation of gromacs (Mark Abraham) -- Message: 1 Date: Thu, 17 Mar 2011 12:24:46 +0100 From: Thomas Koller koller-tho...@gmx.de Subject: [gmx-users] installation of gromacs To: gmx-users@gromacs.org Message-ID: 20110317112446.249...@gmx.net Content-Type: text/plain; charset=utf-8 Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- Message: 2 Date: Thu, 17 Mar 2011 22:28:33 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] installation of gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 7640bbf378.4d828...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 17/03/11, Thomas Koller koller-tho...@gmx.de wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float You've installed in /home/local/fftw3... - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib ... but told configure later to look in /home/local/fftw That doesn't work. Even when it does, it's likely that you'll still need to look at the last few hundred lines of config.log to actually diagnose the problem... Mark iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110317/69c249d5/attachment-0001.html -- Message: 3 Date: Thu, 17 Mar 2011 12:31:04 +0100 From: Diego Enry diego.e...@gmail.com Subject: Re: [gmx-users] installation of gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: aanlktin+hhonkdrxnwd4qpvsrojaxuhu3a4jnasuu...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 You got this wrong export CPPFLAGS=-I/home/local/fftw/include export LDFLAGS=-L/home/local/fftw/lib replace by this export CPPFLAGS=-I$HOME/local/fftw/include export LDFLAGS=-L$HOME/local
[gmx-users] including non standard amino acid CSD in topology file
hello I am using OPLS AA FF and my protein contains a non standard amino acid CSD for which the topology parameters are not present . Can someone tell how to include CSD into topology file? ashu -- 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
Re: [gmx-users] including non standard amino acid CSD in topology file
ashutosh srivastava wrote: hello I am using OPLS AA FF and my protein contains a non standard amino acid CSD for which the topology parameters are not present . Can someone tell how to include CSD into topology file? http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin ashu -- 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/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
[gmx-users] Re: surface tension
Dear Elisabeth, I'm going to make some general remarks on what I would consider a reasonable set of choices for such simulations: (1) 3x3 nm in the xy plane seems perfectly fine to me if your model systems is made up of some well-behaved molecular liquid, alkanes for instance. (2) GROMACS manual describes the Ewald geometry option 3dc for such slab model systems if long range corrections are to be applied (3) whether or not the NVT ensemble is adequate for such simulations is arguable, but definitely applying a plain isotropic NpT coupling introduces errors. take a look at the size of your system using g_energy, probably it shrank in all three directions due to the vacuum in the z-direction. again: either try NVT or use a surface tension coupling (setting compressibility to zero in the z direction to keep the box length constant in that direction) (4) surface tension should be a positive number, meaning that creating a surface requires some amount of energy. best regards, André On Wed, Mar 16, 2011 at 8:31 PM, Elisabeth katesed...@gmail.com wrote: Dear Dr. Andre F. de Moura, Thanks for your invaluable help. I folloed your instructions and made a 3 nm box of alkane (125 molecules) which gives the actual density of material, and increased the size in Z direction. i. e 3X3X6 then did a 8 ns NPT with parrinello-rahman algorithm. I dont know why I am getting negative surface tension. However, the gamma I get from formula Lz=6nm n=2, gamma: 6/2(Pzz - 1/2(Pxx + Pyy)) is almost identical to #Surf*SurfTen divided by 2 values. 0- My question is, the system I have now 3x3x6 is in no way similar to bilayers ( where the structure of system shows a planar surface parrale to XY. Is this because I am studying a pure system? making it different from bilayer study? 1- negative results are because I did not perform NVT? I am interested in NPT to see the effect of pressure on surface tension. does NPT work with surface tenio studies in gromcas? 2- In your previous message you pointed that if the empty region is large enough periodicity no longer affects the system during a typical MD simulation, except for the other two directions. My question is given the 3 nm box size, the empty region in X and Y are also larger than cut-off ! Do I need to work with a 1 nm box size ( because of using 1.1 nm cut offs) instead of 3nm to make sure only in Z direction BC is not working? 3- I am not sure if ~ -3 or ~ -1.7 is the actual surface tension value I should consider. Please see the averages for different time periods. In other words I dont know over how many steps I need to read the average. 4- You suggested to turn off long range interactions, Does that mean PME is not needed? Please see the mdp file below. Thank you so much for you time. Best regards, 8 ns (4 000 000 steps, 0.002 dt) NPT on a box of 3 nm replicated by nbox 112 in Z: Statistics over 351 steps [ 1000.0001 thru 8000.0005 ps ], 3 data sets All averages are exact over 351 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) 20.2098 375.159 375.158 -0.00039324 -2.75268 Density (SI) 616.449 9.13759 9.13759 -3.21055e-06 -0.0224739 #Surf*SurfTen -1.69698 5074.59 5074.08 -0.0354603 -248.222 Statistics over 301 steps [ 2000.0001 thru 8000.0005 ps ], 2 data sets All averages are exact over 301 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) 20.2281 375.189 375.18 -0.00145544 -8.73263 #Surf*SurfTen -1.18619 5062.76 5062.55 -0.0265989 -159.593 Statistics over 251 steps [ 3000.0002 thru 8000.0005 ps ], 2 data sets All averages are exact over 251 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) 20.1216 374.81 374.795 -0.00236499 -11.825 #Surf*SurfTen -3.98186 5055.47 5055.43 -0.013803 -69.0151 From formula: -1.89 bar nm Statistics over 201 steps [ 4000.0002 thru 8000.0005 ps ], 2 data sets All averages are exact over 201 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) 20.0417 376.748 376.725 -0.00359389 -14.3756 #Surf*SurfTen -6.07893 5074.92 5074.89 -0.0160507 -64.2028 Statistics over 151 steps [ 5000. thru 8000.0005 ps ], 2 data sets
[gmx-users] PMF for Carbohydrate-Protein
Dear All, I'm running set of umbrella sampling simulations to get the PMF of a disaccharide binding to a protein. I followed the tutorial provided by Justin and changed the values of necessary parameters according to my system. The mdp file for umbrella sampling simulations is as follows: --- ; Pull code pull= umbrella pull_geometry = distance ; can't get PMF with direction pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = active_site pull_pbcatom0 = 575 pull_group1 = new pull_pbcatom1 = 1500 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 750 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps Active site in the pull_group0 being the residues in the binding site and new in the pull_group1 being the disaccharide. Initially I did an SMD run where I separated the disaccharide from the binding upto 1.5nm in distance. When I started running the umbrella sampling simulations, I used the conformations with approximately 0.1nm difference starting from an initial separation of 0.3nm between the binding site residues and disaccharide. My question is: when I run g_wham and get the profile, the pmf reaches a plateau, but its not completely horizontal. It drops down a little. Is it acceptable to have the pmf reach a plateau but not completely horizontal? In the histogram, the first two windows have good overlap and are narrow distributions where as the later windows are spread out. I have tried to decrease the distance from 0.1 nm to 0.05 nm and still the sampling around 0.5-0.75 of Xi region does not sample well. Is there anything that you could suggest? I have uploaded the plots of profile and histograms. PMF Plot link: http://img801.imageshack.us/i/pmf.png/ Histogram link: http://img217.imageshack.us/i/histoy.png/ Thanks for your time Sai Ramadugu -- 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
[gmx-users] g_wham PMF profile
Dear all, thanks a lot for your suggestions that give me the possibility to improve my calculation. All the best Anna -- 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
Re: [gmx-users] PMF for Carbohydrate-Protein
Sai Kumar Ramadugu wrote: Dear All, I'm running set of umbrella sampling simulations to get the PMF of a disaccharide binding to a protein. I followed the tutorial provided by Justin and changed the values of necessary parameters according to my system. The mdp file for umbrella sampling simulations is as follows: --- ; Pull code pull= umbrella pull_geometry = distance ; can't get PMF with direction pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = active_site pull_pbcatom0 = 575 pull_group1 = new pull_pbcatom1 = 1500 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 750 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps Active site in the pull_group0 being the residues in the binding site and new in the pull_group1 being the disaccharide. Initially I did an SMD run where I separated the disaccharide from the binding upto 1.5nm in distance. When I started running the umbrella sampling simulations, I used the conformations with approximately 0.1nm difference starting from an initial separation of 0.3nm between the binding site residues and disaccharide. My question is: when I run g_wham and get the profile, the pmf reaches a plateau, but its not completely horizontal. It drops down a little. Is it acceptable to have the pmf reach a plateau but not completely horizontal? It looks like you just have a very rocky PMF, indicating that you probably haven't sampled sufficiently (i.e., the simulations are probably too short). In the histogram, the first two windows have good overlap and are narrow distributions where as the later windows are spread out. I have tried to decrease the distance from 0.1 nm to 0.05 nm and still the sampling around 0.5-0.75 of Xi region does not sample well. Is there anything that you could suggest? More windows and/or longer simulations. -Justin I have uploaded the plots of profile and histograms. PMF Plot link: http://img801.imageshack.us/i/pmf.png/ Histogram link: http://img217.imageshack.us/i/histoy.png/ Thanks for your time Sai Ramadugu -- 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/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
Re: [gmx-users] lipopeptide problem
Hi Felix, Thank you for your help. Hi Justin, I did not want to write a long e-mail describing what I did and what did not work. All I wanted to learn was whether there was some more detailed information somewhere that I can reach. You do not have to reply to an email if you feel it is not worth it. Lecturing me on willingness is crossing the line. How do you know how much I tried? Anyhow, thanks for your earlier help, but you can simply skip my future postings. Best regards, Deniz On Thu, Mar 17, 2011 at 12:00 AM, Justin A. Lemkul jalem...@vt.edu wrote: Emine Deniz Tekin wrote: Hi GROMACS Users, I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I simulated a peptide before but this is the first time I am trying to combine a lipid with a peptide (to get a lipo-peptide). I would be really happy if you could help me out with the following question I am tring to create a louroic acid connected to and an 8-redidue peptide. To create residues, I used ARGUSLAB . For the louric acid I used BERGER lipid parameters. Then, as described in KALP-15 in DPPC tutorial, I combined ffbonded.itp and ffnonbonded.itp with lipid.itp. I also adjusted the topol.top files as described in the manual. But this procedure did not yet give me an attached louric acid and peptide. I Nor should you expect it to. Building the parent force field does not give you a topology describing some molecular system. still have to play with the aminoacids.hdb, aminoacids.rtp, residuetypes.dat, atomtypes.atp, and specbond.dat files. I would appreciate if you could let me know how to modify these files, especially the aminoacids.hdb file. I tried several things but it not See the manual, section 5.6.4. The contents and format are discussed at length. work. Note that, I applied the suggestions in http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, but it was not sufficient. If you want free help, you will have to do substantially better than it was not sufficient. What is not clear? What have you tried and what was the result? If you want free help, you've got to demonstrate a willingness to do some work on your own. -Justin Best regards Deniz -- 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/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 -- 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
Re: [gmx-users] lipopeptide problem
Emine Deniz Tekin wrote: Hi Felix, Thank you for your help. Hi Justin, I did not want to write a long e-mail describing what I did and what did not work. All I wanted to learn was whether there was some more detailed information somewhere that I can reach. You do not have to reply to an email if you feel it is not worth it. Lecturing me on willingness is crossing the line. How do you know how much I tried? Anyhow, thanks for your earlier help, but you can simply skip my future postings. I'll respond one last time then, if for no other reason but to defend myself against being considered a complete jerk. I was sincerely trying to help, and in order to do so, I needed to extract a lot more information than what you had provided. I could certainly type out a procedure, step by step for you, which would be rather lengthy (because there are several ways to do this, each based upon a couple different assumptions which need to be considered), and then have it turn out that you've done that and come across some error for one reason or another, and all I've done is waste both of our time and spammed everyone's inbox with an unnecessary message. Instead, I wanted to know what you had done. Even if it's long, it makes the process of helping you exponentially faster in the end. There are dozens of threads in the list archive in recent months alone that go one for dozens of messages, all because the original user is not providing adequate or accurate detail of their problem and their ideas. Leaving us to guess serves no one. But truly, if you don't want me to attempt to help, I certainly won't. If trying to help you both solve your problem and be more efficient is seen as a lecturing and/or crossing the line, then I won't attempt to do either. -Justin Best regards, Deniz On Thu, Mar 17, 2011 at 12:00 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Emine Deniz Tekin wrote: Hi GROMACS Users, I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I simulated a peptide before but this is the first time I am trying to combine a lipid with a peptide (to get a lipo-peptide). I would be really happy if you could help me out with the following question I am tring to create a louroic acid connected to and an 8-redidue peptide. To create residues, I used ARGUSLAB . For the louric acid I used BERGER lipid parameters. Then, as described in KALP-15 in DPPC tutorial, I combined ffbonded.itp and ffnonbonded.itp with lipid.itp. I also adjusted the topol.top files as described in the manual. But this procedure did not yet give me an attached louric acid and peptide. I Nor should you expect it to. Building the parent force field does not give you a topology describing some molecular system. still have to play with the aminoacids.hdb, aminoacids.rtp, residuetypes.dat, atomtypes.atp, and specbond.dat files. I would appreciate if you could let me know how to modify these files, especially the aminoacids.hdb file. I tried several things but it not See the manual, section 5.6.4. The contents and format are discussed at length. work. Note that, I applied the suggestions in http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, but it was not sufficient. If you want free help, you will have to do substantially better than it was not sufficient. What is not clear? What have you tried and what was the result? If you want free help, you've got to demonstrate a willingness to do some work on your own. -Justin Best regards Deniz -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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
[gmx-users] thickness of interface
Dear GROMACS user, Hello. I am new to molecular dynamics simulation, and also to simulation of interface. Recently I have simulated liquid-vapor interface of heptane in a slab with NVT ensemble, and liquid-liquid inteface of water-heptane in NPzAT ensemble. I am using GROMOS force field and SPC/E water model. Using g_density, I obtained the density profile of each system across the z direction of my simulation box. I have two questions I want to ask all of you. 1. In GROMACS, how can I calculate the thickness of these interfaces? I have checked through the manual, and I couldn't find any command for this purpose. 2. What is the expression used for calculating the density profile of liquid-vapor and liquid-liquid interface by g_density? I have gone through the gmx_density.c code and unfortunately I couldn't understand it at the moment due to my zero experience in programming. In a paper I saw that one author use this equation to determine the coexistence densities between liquid and vapor interface: rho(z) = 0.5 [rho(liquid) + rho(vapor)] - 0.5 [rho(liquid) - rho(vapor)] tanh [(z-z0)/d]. z is the z direction of the box, z0 is location of the Gibbs dividing surface, and d is the interface thickness. Is the g_density command also based on that equation? Best regards, Widya -- 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
[gmx-users] 1/viscosity in g_energy
Dear GROMACS users and developers,I'm having trouble getting values for my 1/viscosity calculation which obtained from g_energy:g_energy -f md1_vis.edr -o md1_vis_1perv.xvgthe output:Statistics over 101 steps [ 0. through 2000. ps ], 1 data setsAll statistics are over 11 pointsEnergy Average Err.Est. RMSD Tot-Drift---1/Viscosity 0 0 0 0 (m s/kg)gcq#310: "Shoot them in the back now" (The Ramones)Have I done something wrong with my simulation? If that's the case, then this is my mdp parameter:cpp = /lib/cppinclude = -I../topintegrator = mddt = 0.002nsteps = 1nstxout = 100nstvout = 100nstlog = 1000nstenergy = 100nstxtcout = 100xtc_grps = System energygrps = System nstlist = 10 ns_type = gridrlist = 1.0; PME chosen as the best option to calculate viscosity ;coulombtype = PMErcoulomb = 1.0rvdw = 1.4pbc = xyztcoupl = berendsentc-grps = System tau_t = 0.1; temperature supposed to set to 20*C @ 293.15 K as reference work ; ref_t = 293.15Pcoupl = nogen_vel = yesgen_temp = 298.15gen_seed = 173529constraints = none; NEMD ;acc_grps = systemaccelerate = 0.1 0.0 0.0cos_acceleration = 0.02Any suggestion are most welcomed and thank you in advance!MUHAMMAD ALIF MOHAMMAD LATIFLaboratory of Theoretical and Computational ChemistryDepartment of ChemistryFaculty of ScienceUniversiti Putra Malaysia43400 UPM Serdang, SelangorMALAYSIA -- 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
Re: [gmx-users] 1/viscosity in g_energy
Alif M Latif wrote: Dear GROMACS users and developers, I'm having trouble getting values for my 1/viscosity calculation which obtained from g_energy: g_energy -f md1_vis.edr -o md1_vis_1perv.xvg the output: Statistics over 101 steps [ 0. through 2000. ps ], 1 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- 1/Viscosity 0 0 0 0 (m s/kg) gcq#310: Shoot them in the back now (The Ramones) Have I done something wrong with my simulation? If that's the case, then this is my mdp parameter: This bug has been fixed in the development version of the code. You can download it from the git repository: http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Stable_version -Justin cpp = /lib/cpp include = -I../top integrator = md dt = 0.002 nsteps = 1 nstxout = 100 nstvout = 100 nstlog = 1000 nstenergy = 100 nstxtcout = 100 xtc_grps = System energygrps = System nstlist = 10 ns_type = grid rlist = 1.0 ; PME chosen as the best option to calculate viscosity ; coulombtype = PME rcoulomb = 1.0 rvdw = 1.4 pbc = xyz tcoupl = berendsen tc-grps = System tau_t = 0.1 ; temperature supposed to set to 20*C @ 293.15 K as reference work ; ref_t = 293.15 Pcoupl = no gen_vel = yes gen_temp = 298.15 gen_seed = 173529 constraints = none ; NEMD ; acc_grps = system accelerate= 0.1 0.0 0.0 cos_acceleration = 0.02 Any suggestion are most welcomed and thank you in advance! MUHAMMAD ALIF MOHAMMAD LATIF Laboratory of Theoretical and Computational Chemistry Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA -- 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/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
[gmx-users] Re: change in structure after simulation
Hi, I did a simulation of 5ns ... after viewing the trajectory in VMD , some loop regions seems to be stretched like a straight wire.. But when I made a movie using trjconv and viewed in pymol.. the structure seems to be fine.. So, shall I continue my analysis assuming the structure to be fine ... -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- 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
Re: [gmx-users] Re: change in structure after simulation
bharat gupta wrote: Hi, I did a simulation of 5ns ... after viewing the trajectory in VMD , some loop regions seems to be stretched like a straight wire.. But when I made a movie using trjconv and viewed in pymol.. the structure seems to be fine.. So, shall I continue my analysis assuming the structure to be fine ... http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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/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
