Re: [gmx-users] Announce: Project - Evolutionary Algorithm with Gromacs, Initial results
Nice Job Rodrigo! Your results are very interesting and your implementation of EA algorithm to work with Gromacs is a very relevant contribution. Congratulations! -- Prof. Dr. Alexandre Suman de Araujo Departamento de Física Instituto de Biociências, Letras e Ciências Exatas - IBILCE Universidade Estadual Paulista e-mail: asara...@ibilce.unesp.br Phone: +55 (17) 3221-2566/3221-2240 Em 16-01-2012 13:44, Rodrigo Faccioli escreveu: We would like to announce the first version of a mono-objective algorithm that use GROMACS for Protein Structure Prediction (PSP). Although it is initial version, it was compared with other methodologies. These results were sent to WCCI [1] congress. We would like to share them with who are interested. We are looking for ideas and suggestions to add to this project. The source-code of this algorithm is [2]. Now, we are developing NSGAII algorithm, a multi-objective concept, to work with PSP. All objectives are computed with GROMACS. [1] http://www.ieee-wcci2012.org/ [2] https://gitorious.org/protpred-gromacs Best Regards, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 -- 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] Convert drug Charmm topology to Gromacs
Why don't you post this in User Contribution area of Gromacs Website? I think this is something that could interest a lot of people. Cheers -- Prof. Dr. Alexandre Suman de Araujo Departamento de Física Instituto de Biociências, Letras e Ciências Exatas - IBILCE Universidade Estadual Paulista e-mail: asara...@ibilce.unesp.br Phone: +55 (17) 3221-2566/3221-2240 Em 24-08-2011 15:55, Fabian Casteblanco escreveu: Hello Steven Neumann, I recently converted CGenFF parameters into files that are used by Gromacs. If this is what you need, shoot me an email and I can provide you with the data sets. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.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: Convert drug Charmm topology to Gromacs
Hi Fabian As far as I know, the way to send your contribution is contacting someone who administrate the website. I think Justin is one of them. Probably some of them are reading us and can help you. Cheers -- Prof. Dr. Alexandre Suman de Araujo Departamento de Física Instituto de Biociências, Letras e Ciências Exatas - IBILCE Universidade Estadual Paulista e-mail: asara...@ibilce.unesp.br Phone: +55 (17) 3221-2566/3221-2240 Em 25-08-2011 13:18, Fabian Casteblanco escreveu: Hello Dr. Alexandre Suman de Araujo, I am not sure how to upload to Gromacs User Contribution. I see downloadable files but not place to upload. Do you have the link where I can upload the files? Thanks, Fabian On Wed, Aug 24, 2011 at 2:55 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello Steven Neumann, I recently converted CGenFF parameters into files that are used by Gromacs. If this is what you need, shoot me an email and I can provide you with the data sets. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.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] position restraints and out of bounds atom index
Since anybody helped me with this issue and I solved the problem, I'll report the solution here to contribute with the comunity. As I pointed in the original e-mail, the problem was the difference between the numbering scheme of .gro file and .itp file. I created 3 .pdb files, one for each chain and with pdb2gmx I created 3 .gro files. With these 3 .gro files I created 3 .ndx files with the groups I'd like to apply PR and from these .ndx files I created the PR .itp files, now with the numbering agreeing with the one of the topology files. The include of these PR.itp files in .top file is the same I mentioned in the original e-mail. With this, everything worked fine. Cheers ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Em 16-10-2010 15:41, Alexandre Suman de Araujo escreveu: Hi all I'm trying to simulate a system with 3 chains (A, H and L). Pb2gmx gave me 3 .itp files (one for each chain), each one with atom number starting from 1, and a .top file with these 3 .itp included. It gave me also a .gro file with the 3 chains numbered consecutively (the atom number does not restart from 1 for each chain). With this .gro file I made an index file using make_ndx with 3 groups containing the backbone of each chain. With this index file I built 3 position restraint files with genrestr, one for each chain. Following the instructions from website, I removed the #ifdef POSRES/#include/#endif lines from the end of the .itp file of each chain and added them directly in the .top file as shown below: ; ;File 'proteina.gro.top' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Thu Oct 14 14:22:01 2010 ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.1 ; ;Command line was: ;pdb2gmx -f 2R29CL_original.pdb -o protein.gro -p proteina.gro -his -ignh ; ;Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp ; Include chain topologies #include proteina.gro_Protein_chain_A.itp ; Include Position restraint file for chain A #ifdef POSRES #include posre_Protein_chain_A.itp #endif #include proteina.gro_Protein_chain_H.itp ; Include Position restraint file for chain H #ifdef POSRES #include posre_Protein_chain_H.itp #endif #include proteina.gro_Protein_chain_L.itp ; Include Position restraint file for chain L #ifdef POSRES #include posre_Protein_chain_L.itp #endif ; Include water topology #include oplsaa.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include oplsaa.ff/ions.itp [ system ] ; Name ENVELOPE PROTEIN E; HEAVY CHAIN OF FAB 1A1D-2; LIGHT CHAIN OF FAB 1A1D-2 in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_H 1 Protein_chain_L 1 SOL59 SOL97 SOL95 SOL 30308 NA 91 CL 97 When I run a simulation without the define = -DPOSRES definition in the .mdp file, grompp runs ok. However, when I say in .mdp file to use position restraints grompp give me the following error: Fatal error: [ file posre_Protein_chain_H.itp, line 334 ]: Atom index (3221) in position_restraints out of bounds (1-3212). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I know that this was already discussed in list but nothing described there worked. It is clear that the problem is due to the different numbering scheme of the .gro file and .itp files. The .gro file does not restart the numbering scheme when a new chain starts, on the other hand, the .itp file of each chain starts from 1 in atom number field. Since the position restraint file is generated based on numbering scheme of the .gro file, in some cases (my case is one of them) the PR file refers to a atom number that does not exists in .itp file. I think the way to correct this was generate only one .itp file
[gmx-users] position restraints and out of bounds atom index
Hi all I'm trying to simulate a system with 3 chains (A, H and L). Pb2gmx gave me 3 .itp files (one for each chain), each one with atom number starting from 1, and a .top file with these 3 .itp included. It gave me also a .gro file with the 3 chains numbered consecutively (the atom number does not restart from 1 for each chain). With this .gro file I made an index file using make_ndx with 3 groups containing the backbone of each chain. With this index file I built 3 position restraint files with genrestr, one for each chain. Following the instructions from website, I removed the #ifdef POSRES/#include/#endif lines from the end of the .itp file of each chain and added them directly in the .top file as shown below: ; ; File 'proteina.gro.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Oct 14 14:22:01 2010 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.1 ; ; Command line was: ; pdb2gmx -f 2R29CL_original.pdb -o protein.gro -p proteina.gro -his -ignh ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp ; Include chain topologies #include proteina.gro_Protein_chain_A.itp ; Include Position restraint file for chain A #ifdef POSRES #include posre_Protein_chain_A.itp #endif #include proteina.gro_Protein_chain_H.itp ; Include Position restraint file for chain H #ifdef POSRES #include posre_Protein_chain_H.itp #endif #include proteina.gro_Protein_chain_L.itp ; Include Position restraint file for chain L #ifdef POSRES #include posre_Protein_chain_L.itp #endif ; Include water topology #include oplsaa.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include oplsaa.ff/ions.itp [ system ] ; Name ENVELOPE PROTEIN E; HEAVY CHAIN OF FAB 1A1D-2; LIGHT CHAIN OF FAB 1A1D-2 in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_H 1 Protein_chain_L 1 SOL59 SOL97 SOL95 SOL 30308 NA 91 CL 97 When I run a simulation without the define = -DPOSRES definition in the .mdp file, grompp runs ok. However, when I say in .mdp file to use position restraints grompp give me the following error: Fatal error: [ file posre_Protein_chain_H.itp, line 334 ]: Atom index (3221) in position_restraints out of bounds (1-3212). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I know that this was already discussed in list but nothing described there worked. It is clear that the problem is due to the different numbering scheme of the .gro file and .itp files. The .gro file does not restart the numbering scheme when a new chain starts, on the other hand, the .itp file of each chain starts from 1 in atom number field. Since the position restraint file is generated based on numbering scheme of the .gro file, in some cases (my case is one of them) the PR file refers to a atom number that does not exists in .itp file. I think the way to correct this was generate only one .itp file for the 3 chains, or one .gro file for each chain and use them to create the PR .itp files. However, I don't know how to do any of these 2 tasks using pdb2gmx. Could anyone help me with this issue? There is any other program in Gromacs package that I should use to fix this problem? Best regards. -- Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Novo Webmail IFSC -- 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] vanadium non-bonded parameters
Hi Gonçalo If you do not find the parameters for vanadium, you could try to develop them using experimental physical chemistry properties of the ion and MD simulations. In the following reference you can find a suitable method to develop them that worked for me in the development of Pb and Cd ion parameters: Alexandre S. de Araujo,*,† Milton T. Sonoda,† Oscar E. Piro,‡ and Eduardo E. Castellano, Development of New Cd2+ and Pb2+ Lennard-Jones Parameters for Liquid Simulations, J. Phys. Chem. B 2007, 111, 2219-2224 Cheers ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Em 24-09-2010 16:21, Gonçalo C. Justino escreveu: Dear gmx'ers, Does anyone know of any (published or not) non-bonded parameters for vanadium species for any of the forcefields implemented in GROMACS ? If not, my question is: what is the meaning of the null values for sigma and epsilon in, e.g., amber03, for Fe: FE 26 55.000. A 0.0e+00 0.0e+00 [from the ffnonbonded.itp file] Thks for any help, Gonçalo -- 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] Problem with removing COM translation
Em 13-08-2010 14:24, ms escreveu: On 12/08/10 15:25, Alexandre Suman de Araujo wrote: I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom fixed at the center of the sphere. The protein can move without any restriction. To prevent the separation between protein and the water globule, I defined comm_grps = Protein Non-Protein in my .mdp file (I've also used the same groups in temperature coupling as suggested in GMX manual). However, when I run the simulation the protein COM moves away from the center (where it is in the beginning of the simulation) of the water sphere. The movement of COM of the water sphere is small (less than 1 angstron). For simulations of 5ns this translation is about 2 angstrons and for a 14 ns simulation it is more than 10 angstrons. Does anyone could help me with this issue? As far as I know, the remove of COM motion is made by subtracting the COM velocity from the velocity of the atoms within the groups defined in comm_grps. Is it possible to really freeze the movement of the COM of some groups in GROMACS to achieve an absolute static COM? Cheers I am just curious but... why are you doing actually all of this instead of using a normal periodic solvent box? The idea is to have less water molecules and, consequently, faster simulations. cheers, m. ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Problem with removing COM translation
Hi Gmxers I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom fixed at the center of the sphere. The protein can move without any restriction. To prevent the separation between protein and the water globule, I defined comm_grps = Protein Non-Protein in my .mdp file (I've also used the same groups in temperature coupling as suggested in GMX manual). However, when I run the simulation the protein COM moves away from the center (where it is in the beginning of the simulation) of the water sphere. The movement of COM of the water sphere is small (less than 1 angstron). For simulations of 5ns this translation is about 2 angstrons and for a 14 ns simulation it is more than 10 angstrons. Does anyone could help me with this issue? As far as I know, the remove of COM motion is made by subtracting the COM velocity from the velocity of the atoms within the groups defined in comm_grps. Is it possible to really freeze the movement of the COM of some groups in GROMACS to achieve an absolute static COM? Cheers -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Distance restraint problem with 4.0.5 version
Mark Abraham escreveu:
Alexandre Suman de Araujo wrote:
Hi Gmxers
Some months ago I performed some simulations, with GMX 3.3.3 version,
where I apply distance restraint between water oxygen atoms and a
static dummy site located at the center of a sphere to keep waters
inside this sphere. After performed an upgrade to GMX 4.0.5 version
this distance restraint scheme stopped to work.
I read distance restraint material in 4.0.5 paper manual and I can't
find any modification reported there.
Looking at gmxdump output from tpr's generated with grompp from 3.3.3
and 4.0.5 versions and the same .mdp, .gro and .top files, I had this:
3.3.3 version: grep -i disre gmxdump3.txt |more
disre= Simple
disre_weighting = Conservative
disre_mixed = FALSE
nstdisreout = 100
functype[468]=DISRES, label= 0, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[469]=DISRES, label= 1, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[470]=DISRES, label= 2, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[471]=DISRES, label= 3, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[472]=DISRES, label= 4, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[473]=DISRES, label= 5, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
.
.
.
functype[724]=DISRES, label= 256, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[725]=DISRES, label= 257, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
functype[726]=DISRES, label= 258, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
0 type=468 (DISRES) 389 392
1 type=469 (DISRES) 393 396
2 type=470 (DISRES) 397 400
3 type=471 (DISRES) 401 404
4 type=472 (DISRES) 405 408
5 type=473 (DISRES) 409 412
.
.
.
256 type=724 (DISRES) 1413 1416
257 type=725 (DISRES) 1417 1420
258 type=726 (DISRES) 1421 1424
4.0.5 version: grep -i disre gmxdump4.txt
disre= Simple
disre_weighting = Conservative
disre_mixed = FALSE
nstdisreout = 100
functype[470]=DISRES, label= 0, type=1, low=
0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac=
1.e+00)
0 type=470 (DISRES) 0 3
It is clear that 3.3.3 version is applying the constraints to all
waters (what is correct) and 4.0.5 to just one. However, I can't find
a way to fix this.
Hmm, the above indicates that 3.3.3 wasn't folding the function type
definitions correctly, and apparently 4.0.5 is folding the types as
well as the references to them. If you're sure you've used the same
.mdp/.top, then please submit a bugzilla
(http://bugzilla.gromacs.org/) and attach a .tar of the .top, .mdp,
.tpr and .gro files.
I'm submitting it in the next minutes.
Also have a look at grep -i disre -C 5 gmxdump4.txt to see if there's
anything interesting in the local contexts of the differences.
The result of this grep:
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= Simple
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
--
functype[465]=LJ14, c6A= 4.00489662e-03, c12A= 4.51127153e-06,
c6B= 4.00489662e-03, c12B= 4.51127153e-06
functype[466]=LJ14, c6A= 3.93701671e-03, c12A= 2.11467386e-06,
c6B= 3.93701671e-03, c12B= 2.11467386e-06
functype[467]=LJ14, c6A= 4.08602087e-03, c12A= 3.19497235e-06,
c6B= 4.08602087e-03, c12B= 3.19497235e-06
functype[468]=CONSTR, dA= 1.0001e-01, dB= 1.0001e-01
functype[469]=CONSTR, dA= 1.0897e-01, dB= 1.0897e-01
functype[470]=DISRES, label= 0, type=1, low= 0.e+00,
up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00)
functype[471]=SETTLE, doh= 1.0001e-01, dhh= 1.6323e-01
fudgeQQ = 1
atomtypes:
atomtype[ 0]={radius= 0.0e+00, volume= 0.0e+00,
surftens=-1.0e+00, atomnumber= 7)}
atomtype[ 1]={radius= 0.0e+00, volume= 0.0e+00,
surftens=-1.0e+00, atomnumber= 1)}
--
excls[2][6..8]={0, 1, 2}
excls[3][9..9]={3}
Dis. Rest.:
nr: 3
[gmx-users] Distance restraint problem with 4.0.5 version
Hi Gmxers Some months ago I performed some simulations, with GMX 3.3.3 version, where I apply distance restraint between water oxygen atoms and a static dummy site located at the center of a sphere to keep waters inside this sphere. After performed an upgrade to GMX 4.0.5 version this distance restraint scheme stopped to work. I read distance restraint material in 4.0.5 paper manual and I can't find any modification reported there. Looking at gmxdump output from tpr's generated with grompp from 3.3.3 and 4.0.5 versions and the same .mdp, .gro and .top files, I had this: 3.3.3 version: grep -i disre gmxdump3.txt |more disre= Simple disre_weighting = Conservative disre_mixed = FALSE nstdisreout = 100 functype[468]=DISRES, label= 0, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[469]=DISRES, label= 1, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[470]=DISRES, label= 2, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[471]=DISRES, label= 3, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[472]=DISRES, label= 4, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[473]=DISRES, label= 5, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) . . . functype[724]=DISRES, label= 256, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[725]=DISRES, label= 257, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) functype[726]=DISRES, label= 258, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) 0 type=468 (DISRES) 389 392 1 type=469 (DISRES) 393 396 2 type=470 (DISRES) 397 400 3 type=471 (DISRES) 401 404 4 type=472 (DISRES) 405 408 5 type=473 (DISRES) 409 412 . . . 256 type=724 (DISRES) 1413 1416 257 type=725 (DISRES) 1417 1420 258 type=726 (DISRES) 1421 1424 4.0.5 version: grep -i disre gmxdump4.txt disre= Simple disre_weighting = Conservative disre_mixed = FALSE nstdisreout = 100 functype[470]=DISRES, label= 0, type=1, low= 0.e+00, up1= 3.e+00, up2= 9.3962e+00, fac= 1.e+00) 0 type=470 (DISRES) 0 3 It is clear that 3.3.3 version is applying the constraints to all waters (what is correct) and 4.0.5 to just one. However, I can't find a way to fix this. Does anyone could help me with this issue? Are there modifications in distance restraint algorithm in 4.0.5 version compared with 3.3.3 version? Or this can be a bug? Thanks -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU
Obviously the HD space has nothing to do with GMX performance (unless it is full, of course), but the use of Ubuntu precompiled packages can affect drastically the GMX performance, especially if you are also using pre-compiled MPI library package. An important rule when you are interested in High Performance Computing: Compile ALL your softwares (the last REALLY stable version) using GOOD compilers (GCC is fine, but if you have access to Intel or Portland ones is better). This rule is highly recommended ALSO to your linux kernel. Never leave the important and easy work of compile your important programs with unknown people! Cheers -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Quoting Justin A. Lemkul jalem...@vt.edu: I don't see how hard disk space of the OS has anything to do with the speed of Gromacs. Are the machines you refer to identical in terms of hardware (CPU, RAM, etc) as well as the compilers used to install the software? I have installed Gromacs under several different OS - Mac, Ubuntu Linux, Yellowdog Linux, and Fedora Linux. The only real speed difference comes from the hardware. -Justin Laercio Pol Fachin wrote: Hi! In a UBUNTU installation in dual boot (with Windows, in my case), GROMACS is approximatedely twice slower than in a installation in an entire HD. If you need to install Linux in dual boot, maybe CentOS is a better choice. Best regards, Laércio Pol-Fachin --- Em *ter, 21/7/09, gmx-users-requ...@gromacs.org /gmx-users-requ...@gromacs.org/* escreveu: 1. comparison of gromacs in CENTOS and UBUNTU (jagannath mondal) Date: Tue, 21 Jul 2009 22:49:12 +0530 (IST) From: jagannath mondal jmondal2...@yahoo.co.in http://br.mc515.mail.yahoo.com/mc/compose?to=jmondal2...@yahoo.co.in Subject: [gmx-users] comparison of gromacs in CENTOS and UBUNTU To: gmx-users@gromacs.org http://br.mc515.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org Message-ID: 410193.9922...@web7906.mail.in.yahoo.com http://br.mc515.mail.yahoo.com/mc/compose?to=410193.9922...@web7906.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi, I was planning to install one of the linux distributions : CENTOS or UBUNTU in our xeon 8-core processor. Can any one suggest which one will be better for Gromacs as far as installation and performance is concerned?ThanksJagannath Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/ - Celebridades http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/ - Música http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/ - Esportes http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php WEBMAIL - IFSC - Instituto de FÃsica de São Carlos ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http
Re: [gmx-users] PDB and GRO files
Hi Jamie. Another (free)options to generate the coordinate files (pdb or gro, they are basically the same and can be converted into another using the trjconv tool) are Molden and VMD. With Molden you can build a molecule from scratch easily. I recommend it to draw small molecules like drugs. VMD (version 1.8.7) has two tools that can be what you are looking for. With Molefacture plugin you can draw small molecules and peptides. With Nanotube Builder plugin you can easily build the CNTs you are interested. To construct fullerenes I don't konw any VMD plugin, but probably somebody has already done some plugin or script to generate this kind of molecules, try to search in google by fullerenes and VMD Cheers -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Quoting Jamie Seyed jamie.se...@gmail.com: Hi Justin, On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Hi, Thanks for your comments. But I do not know how to get (or make) the pdb file if it is not made (let say for a new system). Are you using special software to do that to make a pdb or gro file, before starting the simulation? That's going to depend entirely upon what that system is. Building a protein or peptide is not so trivial. Building a small molecule is fairly straightforward using programs like PRODRG (online) or xLeap (part of AmberTools). That said, if your goal is to simulate some arbitrary small molecules, the previous advice of using pdb2gmx will not apply. You will have to build the topologies yourself. Is the result of using these programs a pdb file or gro.. would you please explain a little bit? The systems that I want to simulate are fullerene and CNT. But before that I will simulate a box of water, spce. In this case is it ok to use spc216.pdb (??) or I should use the programs you mentioned? Sorry for these simple questions.. Another thing: It is not possible for me to open some web-pages that users are referring to (some of them are crucial to get the answer)!! Did you face with the same problem or there is new web-address for them?? If you cite some examples, maybe someone can point you in the right direction. The Gromacs webpage is currently migrating to a new site; old webpages can be accessed by appending old to the URL, i.e. http://oldwww.gromacs.org is the old home page. For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you mentioned, but I can not open links on the page. All of them (check force field for example) can not open with like this message Site settings could not be loaded... Is it the page I should use to get a pdb file for my system?? I really appreciate if you let me know the exact web-address to use PRODRG or xLeap (?). Thanks a lot, Jamie -Justin Thanks for your help, Jamie On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br wrote: Hi, If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation. Answered your question a little more specific, although basically, after you get the pdb file, you need to run the pdb2gmx program. The link above explains more details about it. I hope that this email helped you. Cheers, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br http://laips.sel.eesc.usp.br/ Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Hi, I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files? I appreciate your help for solve my basic problems. Thanks
Re: [gmx-users] Hg2+ ions in ion.itp
You can use the methodology described here and develop your own parameters: Development of new Cd2+ and Pb2+ Lennard-Jones parameters for liquid simulations Author(s): de Araujo AS (de Araujo, Alexandre S.), Sonoda MT (Sonoda, Milton T.), Piro OE (Piro, Oscar E.), Castellano EE (Castellano, Eduardo E.) Source: JOURNAL OF PHYSICAL CHEMISTRY BVolume: 111Issue: 9 Pages: 2219-2224 Regards ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Anirban Ghosh escreveu: Hi ALL, My protein system contains Hg ions. As a result GROMACS4.0.5 is throwing the error Fatal error: Residue 'HG' not found in residue topology database How to solve tis issue? Can I add required parameters in the ions.itp file? If so can someone kindly provide the required parameters for Hg2+ ions. Thanks a lot in advance. Regards, *Anirban Ghosh* *Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India * See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] use of LAN for parallel processing
Hi Mark Do you know any site/paper/book which clearly discuss the use of other network paradigms (infiniband, myrinet, etc) to perform fair parallel MD simulations? Thanks! ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Mark Abraham escreveu: akalabya bissoyi wrote: Thanks gromacs for you replay, can any body provide tutorial/standard protocol how to use of LAN for parallel processing. The canonical guide for doing installations of MPI versions of GROMACS can be found here http://oldwww.gromacs.org/content/view/19/32/ 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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs
Hi There are several works dealing with LIE parametrization to many kinds of systems. In the original formulation of the method, the alpha and beta parameters were considered the same for all studied systems. However, with the application of the method in many cases, it was observed the exigence of different LIE parameters set for different systems. This is obtained, in general, with the methodology which defines a training and a test sets of solutes. I'll point you some references that can help you with this subject: 1 - Aqvist, J., Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J Comput Chem 1996, 17, (14), 1587-1597. 2 - Aqvist, J.; Hansson, T., On the validity of electrostatic linear response in polar solvents. J Phys Chem-Us 1996, 100, (22), 9512-9521. 4 - Almlof, M.; Aqvist, J.; Smalas, A. O.; Brandsdal, B. O., Probing the effect of point mutations at protein-protein interfaces with free energy calculations. Biophys J 2006, 90, (2), 433-442. 5 - Stjernschantz, E.; Marelius, J.; Medina, C.; Jacobsson, M.; Vermeulen, N. P. E.; Oostenbrink, C., Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method. Journal of Chemical Information and Modeling 2006, 46, (5), 1972-1983. 6 - de Araujo, A. S.; Sonoda, M. T.; Piro, O. E.; Castellano, E. E., Development of new Cd2+ and Pb2+ Lennard-Jones parameters for liquid simulations. J. Phys. Chem. B 2007, 111, (9), 2219-2224. Other references can be found therein. Best regards ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Neha Gandhi escreveu: Dear GMX-users, In the Gromacs Drug/Enzyme complex solvation tutorial by John E. Kerrigan , in the end they mention about the LIE calculation. The g_lie program uses LIE equation with default scaling factors a=0.18 and b=0.50 . In the tutorial it is mentioned that For example, b = 0.33 is preferred for polar solutes (drugs) like sugars. What is the reference for these values for polar solutes i.e. sugars.? I would appreciate if there is any example of such calculation done in gromacs. Many thanks, Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Poor parallel performance in Ubuntu 8.04
Hi GMXers Some days ago I reported poor performance of GROMACS parallel runnings over Ubuntu 8.04 and software RAID in a quad-core processor. (http://www.gromacs.org/pipermail/gmx-users/2009-January/039088.html) In a attempt to made some tests in non-raid systems running Ubuntu 8.04, I performed simulations in a dual-quad Xeon box. I ran a simulations using the 8 CPUs (8 process) and the performance was also poor, with a behavior near that observed in the quad-core (some cores with around 80% and the others with less than 30%). If I ran 8 independent simulations, all CPUs show a 100% performance. Does anyone have any experience with this Gromacs+Ubuntu poor parallel performance? I think the problem is due to the use of the generic Ubuntu standard kernel. Maybe if I recompile the kernel I can get a better performance system. However, this is just a guess, and I would like to know if anyone already had this problem and solved it. Thanks -- Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil WEBMAIL - IFSC - Instituto de FÃsica de São Carlos ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Poor parallel performance in Ubuntu 8.04
Quoting Jussi Lehtola jussi.leht...@helsinki.fi: On Wed, 2009-02-04 at 18:01 -0200, Alexandre Suman de Araujo wrote: Quoting Jussi Lehtola jussi.leht...@helsinki.fi: That's highly unlikely: it would be a severe performance bug, which would have been picked up by the kernel packager. How did you configure the parallel version? What MPI environment did you use? First I used Ubuntu binary packages for Gromacs (3.3.2) and LAM-MPI. After I compiled both with Intel C and Fortran 11.0 compilers. In both cases (binary and compiled), the performed is basicaly the same. In further tests I compiled the Gromacs 4.0 and, again, the performance was the same. Please keep the discussion on the list. Sorry. It was not my intention to open a private contact with you. Try compiling against OpenMPI (or using the binary compiled against it). LAM has been deprecated for many years, and should not be used anymore. Ok. I used LAM because it is recommended in GROMACS documentation, but I´ll try OpenMPI. Also, is your system big enough to allow efficient scaling? Yes. It scales at 100% in an OpenSuse box with equivalent hardware configuration -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Best Regards -- Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil WEBMAIL - IFSC - Instituto de FÃsica de São Carlos ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Software Raid and low GROMACS performance
Hi Martin Martin Höfling escreveu: Am Dienstag, den 20.01.2009, 17:07 -0200 schrieb Alexandre Suman de Araujo: I have two machines with Intel Quad Core processors and Intel motherboards. In the first one I'm running Open Suse with normal partition scheme. In the second I'm running Ubuntu 8.04 with software RAID 1. Hard disk IO should not limit scaling and simulations at all (in most cases...). In my experience, if you use a high output frequency in simulations, the scaling is affected. So I thought that a possible low writing performance of software RAID 1 should reflect in the GROMACS scaling performance. Running a simulations in parallel (4 process, one for each core) in the first computer I have a scaling of almost 100%. The same simulation in the second computer gives me a very worst scaling. In principle, software RAID and RAID functions implemented in chipsets/BIOS require the CPU. Although RAID 1 should be pretty inexpensive and even RAID 5 should create high load in most MD scenarios. Nothing related with system is using high CPU resources. The top utility gives me only 4 mdrun_mpi process using around 70% of each CPU and anything else related to OS using more than 5%. Is it possible that the software RAID is the responsible for this lost in GROMACS performance? Does anybody have experience with this? Is the rest of the Hardware comparable? To further test impact of your RAID, you can easily disable RAID 1 by (temporarily) remove one of the disks. Best Martin The problem is that the computer with low performance is much more powerful (more RAM and more CPU frequency) than the other one which gives me 100% of scaling! To turn off one HD is a good idea that I already had and I should try this ASAP. Thank's ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to treat an isolated iron (Fe 2+)
If you are interested in develop parameters for Fe2+ suitable to your system without huge computational efforts, see this reference: de Araujo, AS; Sonoda, MT; Piro, OE, et al. JOURNAL OF PHYSICAL CHEMISTRY B Volume: 111 Issue: 9 Pages: 2219-2224 Alexandre Zhong Zheng escreveu: hi all I have an isolated iron in the protein. If I don't' put that iron in, everything runs through fine. However, if I put the iron in, the mdrun step (doing energy minimization) will clash. It says segmentation fault and lots of LINCS WARNING. The iron has a +2 charge with four His ligands and one Glu ligand. The total charge for the complex should be +1. Is there a good way to treat this isolated iron? Thanks a lot. Zhong Zheng ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Possible bug with -rerun option
Thanks David. The instantaneous energies are ok. I'll try to submit this to bugzilla. Best regards Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil David van der Spoel wrote: Alexandre Suman de Araujo wrote: Hi GMXers I observed a strange behavior in a simulation of an equilibrated box with 1409 tip3p water molecules using OPLS-AA, PME and GROMACS 3.3.1 in double precision. My .mdp file is as fallow: the problem is in the averaging. since you save coordinates every hundred steps averaging gives a factor 100 difference. Note that the average value in a rerun will never be the same as in the original run since you are missing 99/100 frames. The instantaneous energies should be the same however. Please submit a bugzilla about averaging in mdrun -rerun and edr files resulting from such runs. ; ; Input file ; title = Simulacao de calculo cpp = /lib/cpp dt = 0.001 integrator = mdnsteps = 1 nstcomm = 1 nstxout = 100 nstvout = 100nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 vdwtype = cut-off rvdw= 0.9 tcoupl = berendsenref_t = 300 tc-grps = System tau_t = 0.1 pcoupl = berendsenpcoupltype = isotropic tau_p = 1compressibility = 4.5e-5 ref_p = 1.0 Finishing the simulation I run g_energy in the .edr, obtaining the follow results: Statistics over 10001 steps [ 0. thru 10. ps ], 3 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential *-55852.6*136.692136 -4.75933-47.598 Total-Energy *-45314.7*78.256477.8627 -2.71554 -27.1581 Temperature *299.942*3.153353.14887 0.058173 0.581788 Heat Capacity Cv: 12.4738 J/mol K (factor = 0.000110527) Until here everything is ok. So I used the same .tpr file and -rerun option in mdrun_d in the trajectory from this first simulation. So I ran g_energy in the new .edr file and obtained: Statistics over 10001 steps [ 0. thru 10. ps ], 3 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential *-563.871*5526.065526.05 -4.75933-47.598 Total-Energy *-457.605*4484.564484.55 -2.9575-29.578 Temperature *3.02467*29.645529.6451 0.0512859 0.512911 Heat Capacity Cv: -0.0871562 J/mol K (factor = 96.0644) It can be seen that there are differences of approximately a factor 100 between Average values. In the .log files I saw the follow results: First Simulation: Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 8.90375e+03 -5.73880e+04 -7.13930e+03 *-5.56236e+04 * 1.04571e+04 Total EnergyTemperature Pressure (bar) *-4.51665e+04**2.97643e+02*4.12898e+02 Step Time Lambda 1 10.00.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 8.36435e+03 -5.68959e+04 -7.10656e+03 *-5.56381e+04* 1.05288e+04 Total EnergyTemperature Pressure (bar) *-4.51094e+04**2.99683e+02* -2.69511e+02 == ### == A V E R A G E S == ### == Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 8.68022e+03 -5.74019e+04 -7.13085e+03 *-5.58526e+04* 1.05378e+04 Total EnergyTemperature Pressure (bar) *-4.53147e+04**2.99942e+02*1.07997e+01 Second Simulation (rerun): Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 8.90375e+03 -5.73880e+04 -7.13930e+03 *-5.56236e+04* 1.04594e+04 Total EnergyTemperature Pressure (bar) *-4.51641e+04**2.97709e+02*4.13037e+02 Step Time
Re: [gmx-users] A simple question about reaction-field
Then the ion-solvent LR interaction is included in ion-solvent SR term in g_energy, am I correct? But what means the LR term that appears when I use rlist rcoulomb? Thanks David. Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil David van der Spoel wrote: Alexandre Suman de Araujo wrote: I´m performing a simulation of an ion in water (TIP3P) using reaction field. I define energy_grps = ion sol in my .mdp file. When I use rlist = rcoulomb, no LR terms appear in g_energy list. When I use rlist rcoulomb, these LR terms appear. So, the LR terms obtained using reaction field is the contribution of implicit solvent between rlist and rcoulomb or the contribution of implicit solvent beyond rcloumb, as is said in GMX manual and other reference texts? Thanks No, the LR energy is still the directly computed energy between the R*. The reaction field effect is implicit in the Coulomb potential, except when you have larger molecules and an exclusion correction term is added. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] A simple question about reaction-field
I´m performing a simulation of an ion in water (TIP3P) using reaction field. I define energy_grps = ion sol in my .mdp file. When I use rlist = rcoulomb, no LR terms appear in g_energy list. When I use rlist rcoulomb, these LR terms appear. So, the LR terms obtained using reaction field is the contribution of implicit solvent between rlist and rcoulomb or the contribution of implicit solvent beyond rcloumb, as is said in GMX manual and other reference texts? Thanks -- Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Nitrate ion
Hi GMXers I'm trying to use in my simulations the nitrate ion defined in OPLS force field as atom-types opls_787 and opls_788, but when I look at OPLS bonded parameters in ffoplsaabon.itp I can't find bonds, angles or dihedral parameters with it's bond_type (N and O as defined in ffoplsaanb.itp). Are these bond_types correct? If yes, where are the bond parameters for them? Does anybody know the paper where these parameter were published? Thank's -- Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] theory of MD
Look at these books: Allen, Tildesley. Computer simulation of liquids Frenkel, Smit. Understanding molecular simulation Leach A.R. Molecular modelling. Principles and applications Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil [EMAIL PROTECTED] wrote: Dear all, My question is on the theory of MD. I actually could not find any material which describes in detail about the time integration algorithm. 1) I wanted to know why the time integration algorithm has to be used, I mean the practical benefits of it. I want the reading reference for the same. 2) Also I have seen that there is no appropriate material which describes practically, i mean in detail from the Newtons laws of motion (taking few partiles as example and simulate it theoretically) and how the velocities, positions etc are claculated. I need the material for the same. Kindly give me the references for papers and tutorials. with best wishes Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Locally enhanced sampling
Look at: http://www.gromacs.org/pipermail/gmx-users/2006-January/019356.html Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil Srivastava, Dhiraj (UMC-Student) wrote: does anyone know how we can do locally enhanced sampling with GROMACS? Dhiraj ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] MSD
Well. I think I agree with David 100 cations and 100 anions without solvent (am I correct?)... probably your system is freezing and an evidence of this is that the slope of your MSD graph tends to zero, so your D tends to zero too. But considering what you said about ACFs and RDFs, I think you know what you are doing and I´ll talk about only MSD. Your MSD plot is right for me. It starts with a non-linear part and after (near 1.5 ns) it become reasonable linear. But I think you need more statistic and I suggest you run more 5 ns of simulation the get a better linear part. The differences between values of D calculated with and without fitting is that in the first case you are fitting the Einstein equation (see manual) in hole graph. In the second case you are using times 0-20 and fitting the equation only in this part of the graph and, like you can see on it, the curve have a high slope in the beginning. Actually, you should use the begin-endfit option from 1.5 ns until the end of graph to fit the Einstein equation only to the linear part. About -trestart, it works restarting the initial position of the molecule every X ps. Try to use 1, 5 and 10 ps values for it and see what happen. Well... summarizing... try to run more 5 ns of simulation, run msd using -beginfit from the begin of linear part of your graph, play with t_restart values. I hope I helped you. Cheers Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil Roman Holomb wrote: Dear colleagues, Thanks for reply! Maybe I'm doing something wrong with using g_msd . I have computed MD (5ns) for system containing 100 anion and 100 cation molecules. Results of ACFs, RDFs look good but not MSD So I have 2_emi_BF4_100.tpr, 2_emi_BF4_100.trr, 2_indexEMI.ndx files. Index file contained numbers of EMI-cation molecules. Then I use command: g_msd -f 2_emi_BF4_100.trr -n 2_indexEMI.ndx -s 2_emi_BF4_100.tpr -o 2_emi_BF4_100_msd_EMI_full.xvg -mol 2_emi_BF4_100_msd_full_D_EMI.xvg And I have resulted Diffusion constants fitted from 0 to 5000 (ps) D[EMI]=(0.002+/-0.003)*10-5 cm2/s The resulted MSD graph is included. Then I try to use time 0-20 ps for fitting: g_msd -f 2_emi_BF4_100.trr -n 2_indexEMI.ndx -s 2_emi_BF4_100.tpr -beginfit 0 -endfit 20 -o 2_emi_BF4_100_msd_EMI_0_20.xvg -mol 2_emi_BF4_100_msd_0_20_D_EMI.xvg The resulted D: 0 to 20 (ps) D[EMI]=(0.508+/-0.253)*10-5 cm2/s. But MSD graphs look ideally the same. I'm not sure that program read number of molecules (instead of atoms). option -mol give only D for different molecules but not their average MSD Also -trestart option dosn't work and give me Segmentation Fault... Any comments are advisable. Thanks in advance! Sincerely /Roman ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
