[gmx-users] Problems with solvation in SW (water shell model)
Hello, I'm trying to solvate an OPLSAA methanol molecule in polarizable water shell. Initially I generated a box of pure water using the TIP5P box available in gromacs 4.5. I simulated pure water and I got all the bulk properties in agreement with published results for SW water. In sequence, I used genbox to add the SW water in a 3x3x3 box with a molecule of methanol. By using grompp I received the following error message when I tried minimization Fatal error: Syntax error - File sw.itp, line 36 Last line read: 'LJ Geometric' Found a second defaults directive. Following a suggestion I found on the gmx-forum I commented the following lines of the sw.itp file. [ defaults ] LJ Geometric Done it, I got pre-process the files, but mdrun gave me the segmentation fault: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps= 5000 Segmentation fault: 11-02 nm, Epot= nan Fmax= 1.61425e+04, atom= 2380 Besides I can not minimize the solution, I also noticed that after I have commented the lines of the file sw.itp, I did not get back to simulate the pure water again. Anyone have any tips on how I could solve this problem? Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Charmm foce field and free energy
Dear all, I'm trying to reproduce the hydration free energy of the methanol using the CHARMM force field. However I am getting a value considerably lower than the experimental: 17 kJ mol-1 (the experimental value is 21 kJ mol-1). Am I forgetting some technicality related to the force field? I using a detailed thermodynamic integration procedure, where I decouple Couloumb and van der Waals interactions separately, at lambda intervals of 0.04. I'm using sd integrator and softcore to decouple van der Waals interactions. Other details: NPT, box with 1000 TIP3P water molecules and one methanol molecule, 400ps per window. In a general review I noticed that is not easy to obtain good accuracies in this property. For example, the original paper (J Comput Chem 29: 2543, 2008), is reported a overestimated value of 23.9 kJ mol-1. In J Phys Chem B 110: 17616, 2006, Hess got a underestimated result by 2 kJ mol-1. Shits reported a value of 18.87 kJ mol-1 in J Chem Phys 122: 134508, 2005. These inexact values is inherent to the models or there was any way to improve the accuracy through the protocol used? Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Distance of pull group is larger than half the box size
Hello guys, I have tried to calculate the PMF for a dimer in a rectangular box of dimensions 3 x 3 x 7. However, the simulation stops when the COM separation is above 1.49 (ie half of the smallest dimension of the box. Since I am pulling along the Z axis at a distance that would be up to 3.5 nm. I've tried both pull_geometry, distance and direction, to try to get around this, but I have not been successful. Do I have to use the dimensions of the box as twice the COM distance (in my case: 5 x 5 x 5; to give me r_max = 2.5nm)? Some of you could give me a hand? DIRECTION pull = umbrella pull_geometry= direction pull_dim = Y Y Y pull_group0 = mol_0 pull_group1 = mol_1 pull_rate1 = 0.01 pull_vec1= 0.0 0.0 1.0 pull_k1 = 3000 DISTANCE pull = umbrella pull_geometry= distance pull_dim = Y Y Y pull_group0 = mol_0 pull_group1 = mol_1 pull_rate1 = 0.01 pull_vec1= 0.0 0.0 0.0 pull_k1 = 3000 ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/ -- 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] Silly little question about PMF - g_wham
Hi gmx-users, How do I plot the repulsive part of the PMF between two molecules that are approaching? I have achieved very good curves, but the potential never exceeds the coordinate reaction axis, stopping exactly at 0. Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/ -- 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: Pull code: separating molecules. distance and direction (SOLVED)
Hello, I found out where my mistake. pull_dim is Y Y Y and not N N Y. Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/ On 11 April 2012 10:28, Eudes Fileti fil...@gmail.com wrote: Hello everybody, I have used pull code to separate two molecules in water. The idea is to generate initial configurations for umbrella sampling. Initially I tried to use pull_geometry=distance. I noticed that the vector connecting the two molecules are not remained on the main axis of the box (z). Then I realized that using pull_geometry=direction (with pull_vec1= 0 0 1) I could keep this distance on the z axis. However, the result of the pulling was exactly the same as with pull_geometry=distance, ie, as the molecule moves away from the reference molecule the distance of separation does not remain on the z axis, as I wish. The protocol used was as follows: pull = umbrella pull_geometry= direction pull_dim = N N Y pull_ngroups = 1 pull_group0 = mol_0 pull_weights0= pull_pbcatom0= 0 pull_group1 = mol_1 pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 1.0 pull_init1 = 0.0 pull_rate1 = 0.01 pull_k1 = 1000 Someone could direct me to where I am wrong? Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/ -- 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] Pull code: separating molecules. distance and direction
Hello everybody, I have used pull code to separate two molecules in water. The idea is to generate initial configurations for umbrella sampling. Initially I tried to use pull_geometry=distance. I noticed that the vector connecting the two molecules are not remained on the main axis of the box (z). Then I realized that using pull_geometry=direction (with pull_vec1= 0 0 1) I could keep this distance on the z axis. However, the result of the pulling was exactly the same as with pull_geometry=distance, ie, as the molecule moves away from the reference molecule the distance of separation does not remain on the z axis, as I wish. The protocol used was as follows: pull = umbrella pull_geometry= direction pull_dim = N N Y pull_ngroups = 1 pull_group0 = mol_0 pull_weights0= pull_pbcatom0= 0 pull_group1 = mol_1 pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 1.0 pull_init1 = 0.0 pull_rate1 = 0.01 pull_k1 = 1000 Someone could direct me to where I am wrong? Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/ -- 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: Isovalue for g_spatial representation
Dear Chris, thank you for information, they were very enlightening. Just one more question. Suppose I use an isovalue, say 10, I can say that the drawn surface is 10 times the average number density of solvent molecules? I am using -div option. Bests eef ___ Eudes Eterno Fileti Física da Matéria Condensada Simulação Computacional de Nano-estruturas via Dinâmica Molecular Message: 2 Date: Fri, 29 Oct 2010 19:53:38 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] Isovalue for g_spatial representation To: gmx-users@gromacs.org Message-ID: 20101029195338.kzvrdcvjr440c...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed eef, I wrote g_spatial. If you use the -nodiv option, then the iso-value represents the number of counts in that bin over the entire trajectory divided by the number of frames. Therefore the units would be atomic occupancy counts per frame. Note that, as for all such histograms, the values of isolines and isosurfaces are dependent on bin size. If you use the -div option (default), then the counts (already divided by the number of frames) are further divided by the number of atoms in the selection and then multiplied by the number of cells (similar to dividing by the volume of each cell). It's really a lot like an RDF: a number density per grid divided by the overall system density. It is, however, related to this by some multiplicative constant. You can find that because at the end of a g_density -div run, you will get an output of exactly what this divisor was, so you can go in using awk or whatever you like and modify the values as you see fit, turning values into proper densities if you like. Alternatively, you can run -nodiv and then divide all the the values yourself to get a proper density. Chris. -- original message -- Hello gmx-users. I calculated the spatial distribution functions for my solvent-solute system. However I am in doubt in relation to the isovalue to be used in VMD to control the representation of the surface. The isovalue is admensional number or has some unit? There is some special criterium to choose its value? Thank you in advance. eef -- -- 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! End of gmx-users Digest, Vol 78, Issue 225 ** -- 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] Isovalue for g_spatial representation
Hello gmx-users. I calculated the spatial distribution functions for my solvent-solute system. However I am in doubt in relation to the isovalue to be used in VMD to control the representation of the surface. The isovalue is admensional number or has some unit? There is some special criterium to choose its value? Thank you in advance. eef ___ Eudes Eterno Fileti Física da Matéria Condensada Simulação Computacional de Nano-estruturas via Dinâmica Molecular -- 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_velacc problem
Hi Florian, in fact I had already realized that it was possible to calculate the VACF without using the -m option (although this option was important for my calculations). I have not received any attachment, have you send me something? If necessary, please, send it to my email. Following your suggestions I changed the indicated lines and recompiled the program. Now I gotta get VACF! It's working fine even including the -m flag. Thank you. eef ___ Eudes Eterno Fileti Física da Matéria Condensada Simulação Computacional de Nano-estruturas via Dinâmica Molecular -- 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: g_velacc problem (Florian Dommert)
Dear Florian, thanks for the help. I wonder just one more thing. Is it possible to obtain the lateral diffusion coefficient in a specific plane (say xy) using g_velacc? Or it is only possible with g_msd? Bests eef ___ Eudes Eterno Fileti Física da Matéria Condensada Simulação Computacional de Nano-estruturas via Dinâmica Molecular -- 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: Re: Re: g_velacc problem (Florian Dommert)
Dear Florian, thanks again. I have worked with confined systems, where motion in a given direction/plane is preferred. The accuracy of the MSD approach for calculating the diffusion coefficient has been questioned for this my system. So I need to calculate D via VACF. Considering my limited abilities to programming I wonder if it would be possible to you send me more details about the changes that I should implement the program. Any help will be very useful! Bests eef ___ Eudes Eterno Fileti Física da Matéria Condensada Simulação Computacional de Nano-estruturas via Dinâmica Molecular Message: 1 Date: Thu, 14 Oct 2010 17:22:38 +0200 From: Florian Dommert domm...@icp.uni-stuttgart.de Subject: Re: [gmx-users] Re: g_velacc problem (Florian Dommert) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cb7203e.1020...@icp.uni-stuttgart.de Content-Type: text/plain; charset=ISO-8859-1 -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/14/2010 04:41 PM, Eudes Fileti wrote: Dear Florian, thanks for the help. I wonder just one more thing. Is it possible to obtain the lateral diffusion coefficient in a specific plane (say xy) using g_velacc? Or it is only possible with g_msd? I am not sure, but the MSD is nothing else than the integrated VACF, so if you modify the code correspondingly it should work. The modification shouldn't be that hard, because you just have to prevent summing up a certain direction of the velocity. /Flo Bests eef ___ Eudes Eterno Fileti Física da Matéria Condensada Simulação Computacional de Nano-estruturas via Dinâmica Molecular - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- 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: Re: g_velacc problem (Florian Dommert)
Hi Florian, thank you for your help! I informed at the file.mdp that the velocities should be saved: ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout = 10 nstfout = 0 ; Also, I checked the trajectory using gmxcheck and I got this: Checking file traj.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 7178 Last frame 15 time 3000.000 Item#frames Timestep (ps) Step1500010.02 Time1500010.02 Lambda 1500010.02 Coords 1500010.02 Velocities 1500010.02 Forces 0 Box 1500010.02 So I believe that velocities are OK. I've been using version 4.5 and not version 4.5.1, Do you believe that's the problem? Or it could be memory problem? ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br On 10/12/2010 11:12 PM, Eudes Fileti wrote: Hi everybody, I'm trying to use g_velacc to calculate the diffusion coeficient for my solute. For this, I performed a simple simulation to test such tool. 1000 water molecules, NPT ensemble positions and velocities colected every 0.01ps Gromacs 4.5. However, once I run: g_velacc -f traj -s -n index.ndx -o -m -acflen 1000 -nonormalize I get the following error: Group 0 ( System) has 3000 elements Group 1 (SOL) has 3000 elements Group 2 ( OW) has 1000 elements Group 3 (HW1) has 1000 elements Group 4 (HW2) has 1000 elements Select a group: 1 Selected 1: 'SOL' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Segmentation fault Recently I used g_velacc in gmx 4.0.7 and it worked fine. Now I just tested the gmx4.5.1 version for you and it also worked. So it seems that there is something wrong with your trajectory. Are you sure that velocities were saved, which is not the case for an xtc file. You have to explicitly define nstvout in your mdp file, that tells gromacs how often the velocities should be written to the trr file. /Flo I've tried several things. I changed flag values. I tried the -mol option. I tried converting a trajectory to another format (.trj). I tried using the version 3.3.3 of g_velacc. Nothing worked, always the same error. Could someone give me a hand? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- 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_velacc problem
Hi everybody, I'm trying to use g_velacc to calculate the diffusion coeficient for my solute. For this, I performed a simple simulation to test such tool. 1000 water molecules, NPT ensemble positions and velocities colected every 0.01ps Gromacs 4.5. However, once I run: g_velacc -f traj -s -n index.ndx -o -m -acflen 1000 -nonormalize I get the following error: Group 0 ( System) has 3000 elements Group 1 (SOL) has 3000 elements Group 2 ( OW) has 1000 elements Group 3 (HW1) has 1000 elements Group 4 (HW2) has 1000 elements Select a group: 1 Selected 1: 'SOL' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Segmentation fault I've tried several things. I changed flag values. I tried the -mol option. I tried converting a trajectory to another format (.trj). I tried using the version 3.3.3 of g_velacc. Nothing worked, always the same error. Could someone give me a hand? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br -- 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_clustsize not recognize the -mol option and ignore the index file
Hello everybody, I'm using g_clustsize to analyze clusters formed in my solution. However I noticed that not would get consistent results using the complete trajectory (containing both solvent and solute). To see the aggregation, using g_clustsize, I had to convert my trajectory to a file containing only the solute molecules. That's because -mol option considered all the molecules in the box (ignoring the index file) and as a result I always got a single cluster with all the solvent+solute molecules. Is there a more efficient way to do this? Is this a bug in the program? I've been reading all information on this tool from the gmx-list and I could see some difficulties in dealing with it the way it is. Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br -- 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: Pull geometry direction_periodic not supported
Hi gmx-users I finished a series of pulling runs using the periodic_direction option and when I run the g_wham analysis I received the following message. --- Program g_wham, VERSION 4.5 Source code file: gmx_wham.c, line: 1369 Fatal error: Pull geometry direction_periodic not supported For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Is there any way to circumvent this or should I redo all my simulations with the option of direction instead direction_periodic? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br -- 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] Dipeptide generation problem
Hello everybody, I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue. This dipeptide has a positively charged site (NH3+) and a negatively charged site (COO-). My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to be consistent and produces error when I execute pdb2gmx. The link above presents the PDB and the error message from pdb2gmx (which I have not found similar in the forum). Could someone give me a hand with that? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- 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] Dipeptide generation problem [Justin]
Olá Justin, thank you for responding to my post. I had tried what you mentioned before. All I get is that the some atoms are missing (see error message in the link https://sites.google.com/site/fileti/ ). In fact, as I just want NH3+ (from LYS) and COO- (from ASP), the other atoms are not included in PDB file and this can give error. If I put everything into the same group (1 for example) many of the atoms are deleted by pdb2gmx because they are duplicates. In fact I still do not quite understand the logic of creating a PDB from the aminoacid residues. I've read some tips on the list but still I could not understand. That's it. If you have any suggestion, it will be very useful. Até mais eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- Message: 2 Date: Thu, 26 Aug 2010 09:32:06 -0300 From: Eudes Fileti fil...@ufabc.edu.br Subject: [gmx-users] Dipeptide generation problem To: gmx-users@gromacs.org Message-ID: aanlktikwxuc1g8fq=fqnpfixswadstspha=9qjptd...@mail.gmail.com Content-Type: text/plain; charset=windows-1252 Hello everybody, I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue. This dipeptide has a positively charged site (NH3+) and a negatively charged site (COO-). My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to be consistent and produces error when I execute pdb2gmx. The link above presents the PDB and the error message from pdb2gmx (which I have not found similar in the forum). Could someone give me a hand with that? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100826/0cfce19f/attachment-0001.html -- Message: 3 Date: Thu, 26 Aug 2010 08:36:24 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Dipeptide generation problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4c765fc8.4020...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed Eudes Fileti wrote: Hello everybody, I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue. This dipeptide has a positively charged site (NH3+) and a negatively charged site (COO-). My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to be consistent and produces error when I execute pdb2gmx. The link above presents the PDB and the error message from pdb2gmx (which I have not found similar in the forum). Could someone give me a hand with that? Your .pdb file contains various broken residues (ASP, LYS) and non-sequential numbering (i.e., those broken residues are all numbered 1). Clean up the .pdb and try again. -Justin Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- 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/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: RE: [gmx-users] Dipeptide generation problem [Justin, Mark, Osmair]
Olá, Justin, Mark and Osmair. Thanks for help. Building dipeptide has not been the problem. Actually I need to use atomic coordinates obtained from a previous X-ray crystal structure. For this, I need to give each atom its proper name. That is, I have this: ... ATOM 10C UNK 1 -2.980 6.010 1.900 1.00 0.00 ATOM 11C UNK 1 -2.380 5.770 1.130 1.00 0.00 ATOM 12H UNK 1 -4.050 7.000 1.400 1.00 0.00 ATOM 13H UNK 1 -3.590 7.740 0.930 1.00 0.00 ATOM 14H UNK 1 -4.620 6.540 0.740 1.00 0.00 ATOM 15C UNK 1 -4.930 7.590 2.470 1.00 0.00 ... and I need something like this: ... ATOM 10 CG PHE 1 -2.980 6.010 1.900 1.00 0.00 ATOM 11 CD1 PHE 1 -2.380 5.770 1.130 1.00 0.00 ATOM 12 HD1 PHE 1 -4.050 7.000 1.400 1.00 0.00 ATOM 13 CD2 PHE 1 -3.590 7.740 0.930 1.00 0.00 ATOM 14 HD2 PHE 1 -4.620 6.540 0.740 1.00 0.00 ATOM 15 CE1 PHE 1 -4.930 7.590 2.470 1.00 0.00 ... Of course if I try to use pdb2gmx without assigning these names, the execution fails. I know this should be simple and that there should be several ways to revolve, but it's puzzling me. Is there any software or script I can use to do that automatically? Any hint is very welcome! Até mais eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Dipeptide generation problem [Justin] To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: fb1e9b59.4c772...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 - Original Message - From: Eudes Fileti fil...@ufabc.edu.br Date: Friday, August 27, 2010 2:15 Subject: Re: [gmx-users] Dipeptide generation problem [Justin] To: gmx-users@gromacs.org Olá Justin, thank you for responding to my post. I had tried what you mentioned before. All I get is that the some atoms are missing (see error message in the link https://sites.google.com/site/fileti/ ). In fact, as I just want NH3+ (from LYS) and COO- (from ASP), the other atoms are not included in PDB file and this can give error. If I put everything into the same group (1 for example) many of the atoms are deleted by pdb2gmx because they are duplicates. In fact I still do not quite understand the logic of creating a PDB from the aminoacid residues. I've read some tips on the list but still I could not understand. Have a look some MD tutorial material (doesn't have to be GROMACS). They probably start with a well-formed PDB file. That's probably a better learning experience than trying to read the format description. Alternatively, use a molecule builder (search webpage for suggestions here) to create the coordinates, and then get pdb2gmx to do the rest of the work. The idea behind pdb2gmx is that you don't have to move mountains to get your termini right, and the corresponding topology. If you just give it two adjacent PHE (charged or not), you can tell pdb2gmx what termini you want it to have. Done right, this whole task should not require you to inspect or change a coordinate file at all. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100827/543767bc/attachment-0001.html -- Message: 3 Date: Thu, 26 Aug 2010 16:36:23 + From: Osmair Oliveira osmai...@hotmail.com Subject: RE: [gmx-users] Dipeptide generation problem [Justin] To: gmx-users@gromacs.org Message-ID: snt110-w61a3ea483256a7caf02decc3...@phx.gbl Content-Type: text/plain; charset=windows-1252 Hi Eudes, I do not know how work CHARMM force field, but if you use the following PDB file for your dipeptide using OPLS-AA force field, you can obtain good results!. ATOM 1 N PHE 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 H1 PHE 1 -0.940 0.000 -0.330 1.00 0.00 ATOM 3 H2 PHE 1 0.470 0.820 -0.330 1.00 0.00 ATOM 4 H3 PHE 1 0.470 -0.820 -0.330 1.00 0.00 ATOM 5 CA PHE 1 0.000 0.000 1.460 1.00 0.00 ATOM 6 HA PHE 1 -0.500 0.920 1.790 1.00 0.00 ATOM 7 CB PHE 1 -0.780 -1.200 1.990 1.00 0.00 ATOM 8 HB1 PHE 1 -0.340 -2.120 1.570 1.00 0.00 ATOM 9 HB2 PHE 1 -0.670 -1.250 3.080 1.00 0.00 ATOM 10 CG PHE 1 -2.240 -1.170 1.650 1.00 0.00 ATOM 11 CD1 PHE 1 -3.140 -0.480 2.450 1.00 0.00 ATOM 12 HD1 PHE 1 -2.770 0.040 3.340 1.00 0.00 ATOM 13 CD2 PHE 1
Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]
Hello Justin, thank you for answering! I think I already have done what you suggested when I created my ffbonded.itp and .rtp files. I am sending a piece of my topology and ffbonded.itp files. Follows also the residue from .rtp and the configuration of glycol (.gro) so you can consider where I might be wrong and what I still must do. Thanks again. eef !!! topol.top !!! ; Include forcefield parameters #include charmm27.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Other 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 HCP1 1PA2HOA 1 0.42 1.008 ; qtot 0.42 2 OC311 1PA2OHA 1 -0.6515.9994 ; qtot -0.23 3 CC322 1PA2 CA 1 0.05 12.011 ; qtot -0.18 4 HCA2 1PA2HA1 1 0.09 1.008 ; qtot -0.09 ... [ bonds ] ; aiaj functc0c1c2c3 1 2 1 2 3 1 3 4 1 ... [ pairs ] ; aiaj functc0c1c2c3 1 4 1 1 5 1 1 6 1 ... [ angles ] ; aiajak functc0c1c2 c3 1 2 3 5 2 3 4 5 ... [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 1 2 3 4 9 ... !!! ffbonded.itp !!! [ bondtypes ] ; i j funcb0 kb OC311 HCP11 0.0960 456056.0 ; par22 OH1 H CC322 OC311 1 0.1420 334720.0 ; adm 11/08, glycerol CC322 HCA21 0. 258571.2 ; par22 HA CT2 [ angletypes ] ; i j kfunc th0 cth ub0 cub HCP1OC311 CC312 5 106.00 412.400.0 0.00 ; og 1/06 EtOH IR fit [ dihedraltypes ] ; i j k l funcphi0cp mult HCP1OC311 CC322 HCA29 0.0 0.753 ; og methanol !!! file.rtp !!! [ PA2 ] ; Glycol [ atoms ] HOAHCP10.4201 OHA OC311 -0.6501 CA CC3220.0501 HA1HCA20.0901 HA2HCA20.0901 CB CC3220.0502 HB1HCA20.0902 HB2HCA20.0902 OHB OC311 -0.6502 HOBHCP10.4202 [ bonds ] OHAHOA OHACA CAHA1 CAHA2 CBCA CBHB1 CBHB2 OHB CB HOB OHB !!! conf.gro !!! GROningen MAchine for Chemical Simulation 10 1PA2HOA1 -0.248 -0.048 0.000 1PA2OHA2 -0.177 0.017 0.000 1PA2 CA3 -0.052 -0.052 0.000 1PA2HA14 -0.041 -0.115 0.089 1PA2HA25 -0.041 -0.115 -0.089 1PA2 CB6 0.057 0.054 0.000 1PA2HB17 0.046 0.117 -0.089 1PA2HB28 0.046 0.117 0.089 1PA2OHB9 0.182 -0.015 0.000 1PA2HOB 10 0.253 0.049 0.000 3.0 3.0 3.0 ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- Forwarded message -- From: gmx-users-requ...@gromacs.org Date: Mon, Aug 23, 2010 at 7:00 AM Subject: gmx-users Digest, Vol 76, Issue 113 To: gmx-users@gromacs.org 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. Metallic boundary conditions (poj...@icp.uni-stuttgart.de) 2. Charmm to Gromacs: Polyols force field (Eudes Fileti) 3. Re: Charmm to Gromacs: Polyols force field (Justin A. Lemkul) 4. PMF (abdul wadood) 5. Re: please, how edr data is xdr packed? (Sander Pronk) -- Message: 1 Date: Sun, 22 Aug 2010 17:52:46 +0200 From: poj...@icp.uni-stuttgart.de Subject: [gmx-users] Metallic boundary conditions To: gmx-users@gromacs.org Message-ID: 3e5fe7757a687609503cad715e2a5d15.squir...@www.icp.uni-stuttgart.de Content-Type: text/plain;charset=iso-8859-1 Hi, thank you for your answer. What is then epsilon_r ? regards. -- Message: 2 Date: Sun, 22 Aug 2010 14:42:43 -0300 From: Eudes Fileti fil...@ufabc.edu.br Subject: [gmx-users] Charmm to Gromacs: Polyols force field
Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]
Hello Justin, thanks again. Well, the line 40 is just one of the 36 parameters not found! In this link ( https://sites.google.com/site/fileti/ ) I put the complete files. I know I need to determine which bond type should be called and I believe that it has been done, but I don't know why it's not being found. The order of atoms in the link could be the cause of error? Ie, CA-CB would be different from CB-CA, or HO-OH-CB would be different from CB-OH-HO? If possible you take a quick conferred and gave me some guidance, it would be great! Bests Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC - CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- 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: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark]
Hello Mark thanks for the comments, In fact, what I did was insert the parameters into ffbonded.itp file. What I presented the link above is just the part that I had added (of course there is the line 1495, not shown!). The installation where I started making the change is new, I have not changed anything, just added the lines for the parameters mentioned. Nevertheless, you think I need to re-install the gromacs? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- 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: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark, Justin]
Olá, Mark and Justin. Solved. I did what you suggested and I got all the default values. Muito obrigado! eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- 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] Charmm to Gromacs: Polyols force field
Olá pessoal, Recently, McKerrel published his CHARMM force field to polyols (JCTC, 2009, 5, 1315). I am very interested in using it in GROMACS. For this, I began the transfer of the parameters with the following recipe: 1) All atom types were added to the atomtypes.atp file; 2) All bonded parameters (bonds, angles, ub, dihedral and impropers) were added to the ffbonded.itp file; 3) van der Waals and Coulomb parameters were inserted properly in ffnonbonded.itp; 4) The residues were created in a new file named polyols.rtp. Well, pdb2gmx works fine! It generates the restraints file (posre.itp), configuration file (conf.gro) and topology file (topol.itp). But when I run it in grommp, the default for parameters are not found. Something like: ERROR 6 [file topol.top, line 40]: No default Bond types I know I can insert the parameters by hand in each .top file generated by pdb2gmx. But what I need to do, so that grompp recognizes the default values automatically. Did I forgot some file? I'm making some mistake? Any suggestion is welcome! Muito obrigado! eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- 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] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)
Hello Chris, thanks for the tips, they were very helpful. Now a new problem appeared. I'm trying to separate the two benzene molecules from one another while maintaining the displacement vector aligned with the z axis. For that I have used pull_geometry = direction. However, at the end of the simulation, I notice that the desired alignment (with z) was not maintained. The molecule is pulled away from z and eventually crosses the PBC. I took a good look at gmx-list and noticed that you rode conducting tests with this option. Could you give me a light on this problem too? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Constraint causing system to explode (Warren Gallin) 2. PMF in vacuum (chris.ne...@utoronto.ca) 3. Re: Compile gromacs 4.0.7 with mopac (Stefan Hoorman) 4. vibrational spectra of glucose (Nilesh Dhumal) -- Message: 2 Date: Thu, 27 May 2010 12:12:03 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum To: gmx-users@gromacs.org Message-ID: 20100527121203.orb2sq228s4ow...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: To answer your pbc vs no-pbc question, I suggest that you use pbc=no and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all interactions in direct space with no cutoffs. ## Major comments that you should still investigate 1. There is no need to use a virtual atom, the pull code will use the center of mass. I strongly suggest that you stop using a virtual atom and just use the entire benzene as an argument to the pull code group. I have had difficulties with slightly more complicated setups of this type. 2. In test2.jpg, the system without pbc shows a flat PMF after the cut-off -- exactly what one would expect. The pbc system shows continued interaction -- again what I would expect. So there is nothing actually all that strange here. One would not expect to see such a drastic difference in a high dielectric such as water, but in vacuum I suspect that this is expected. 3. Please clarify what your cutoff was. I don't see a cut-off listed in your .mdp options and leaving this to the default of 1.0 nm is a bad idea because it can lead to confusion a times like this. I might assume that it was 0.7 nm based on test2.jpg, but then see the point #3 below. 4a. I have no idea what -DPOSRES is actually doing for you since I can't see your topology. 4b. Are you sure that pull_dim = N N Y is really what you want? Sometimes one wants to average over X and Y, but I am not sure that you do in this case. 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? ### More minor notes: 5. regarding test1.jpg: a PMF is correct to an additive constant, meaning that you can shift two PMFs relative to one another. These 2 PMFs are therefore less different than they appear in your compaison plot, but they do differ in the slope between 1.0 - 2.0 nm. This is probably just a convergence issue and you will always need to do tests like this. 6. regarding histo.png: can you confirm that the few very short gaussians are due to less sampling in a few windows? In any event, the overlap looks good. Chris -- original message -- Hello Chris, thanks for your attention. I'm sending you some links to some tests I performed. As I said you will notice that depending on the parameter used my simulation shows PMF profiles quite different. Especially what concerns to the difference between the use or not of the PBC. https://sites.google.com/site/fileti/files/test1.jpg https://sites.google.com/site/fileti/files/test2.jpg https://sites.google.com/site/fileti/files/histo.png I have constructed two very similar topologies (ben-a.itp and ben-b.itp) where I put a virtual site in the center of benzene. This sites were restrained to keep my molecules fixed distance desired. The basic details of the simulations are given below:1000 define = -DPOSRES integrator = sd tinit= 0 dt = 0.002 nsteps = 500 or 50 comm-mode= angular nstcomm = 1 comm-grps= System bd-fric = 1 ld-seed = 1993 nstlist = 5 ns_type = simple pbc = no or xyz periodic_molecules = no rlist= 0 coulombtype = Cut-off vdw-type = Cut-off rvdw = 0 DispCorr = no
[gmx-users] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)
Dear Chris, I'm so sorry for surperficial email. You are correct because in the previous message I forgot to mention that now the simulation was performed in water (naturally with PBC). The main parameters of the simulation are given below. As I said, I wish to keep the displacement of the pulled molecule at the z-axis, but I'm not getting with this protocol. For the vacuum I followed the tips you gave me earlier and had success! Thanks eef title = Umbrella pulling simulation integrator = sd dt = 0.002 nsteps = 300 constraint_algorithm = lincs constraints = all-bonds nstlist = 5 ns_type = simple rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = Cut-off Tcoupl = V-rescale tc_grps = system tau_t = 0.1 ref_t = 298 Pcoupl = no pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 pbc = xyz ; Pull code pull = umbrella pull_geometry = direction pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = BEN1 pull_group1 = BEN2 pull_vec1 = 0 0 1 pull_rate1 = 0.001 pull_k1 = 1600 Message: 4 Date: Tue, 08 Jun 2010 08:05:23 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum and pull direction To: gmx-users@gromacs.org Message-ID: 20100608080523.i6oo62he1wwc0...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: You can make my job a whole lot easier! First, please go back through all of the comments that I gave you last time and reply to them one by one. Did you do them? What did you see? Second, please include your new .mdp and some quantitative results to better explain what you see (e.g. your .px file and a description of why the values are not what you expect). Sorry if this sounds annoying, but there's no point in my working in the dark. Chris. -- original message -- Hello Chris, thanks for the tips, they were very helpful. Now a new problem appeared. I'm trying to separate the two benzene molecules from one another while maintaining the displacement vector aligned with the z axis. For that I have used pull_geometry = direction. However, at the end of the simulation, I notice that the desired alignment (with z) was not maintained. The molecule is pulled away from z and eventually crosses the PBC. I took a good look at gmx-list and noticed that you rode conducting tests with this option. Could you give me a light on this problem too? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br Message: 2 Date: Thu, 27 May 2010 12:12:03 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum To: gmx-users@gromacs.org Message-ID: 20100527121203.orb2sq228s4ow...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: To answer your pbc vs no-pbc question, I suggest that you use pbc=no and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all interactions in direct space with no cutoffs. ## Major comments that you should still investigate 1. There is no need to use a virtual atom, the pull code will use the center of mass. I strongly suggest that you stop using a virtual atom and just use the entire benzene as an argument to the pull code group. I have had difficulties with slightly more complicated setups of this type. 2. In test2.jpg, the system without pbc shows a flat PMF after the cut-off -- exactly what one would expect. The pbc system shows continued interaction -- again what I would expect. So there is nothing actually all that strange here. One would not expect to see such a drastic difference in a high dielectric such as water, but in vacuum I suspect that this is expected. 3. Please clarify what your cutoff was. I don't see a cut-off listed in your .mdp options and leaving this to the default of 1.0 nm is a bad idea because it can lead to confusion a times like this. I might assume that it was 0.7 nm based on test2.jpg, but then see the point #3 below. 4a. I have no idea what -DPOSRES is actually doing for you since I can't see your topology. 4b. Are you sure that pull_dim = N N Y is really what you want? Sometimes one wants to average over X and Y, but I am not sure that you do in this case. 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? ### More minor notes: 5. regarding test1.jpg: a PMF is correct to an additive constant, meaning that you can shift two PMFs relative to one another. These 2 PMFs are therefore less different than they appear in your compaison plot, but they do differ in the slope between 1.0 - 2.0 nm. This is probably just a convergence issue and you will always need to do tests like this. 6. regarding histo.png: can you confirm that the few very short
[gmx-users] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)
Hello Chris, thanks for the reply. Below his message commented walkthrough. In your email you asked me for quantitative results. All I have so far is a visual inspection of the pulling trajectory. All I can see are the two molecules moving linearly away from each other in a rectangular box of dimensions 3x3x6nm. However this separation does not occur on the z axis, as I wanted, but in a diagonal way across the faces of the box. Bests eef 1. There is no need to use a virtual atom, the pull code will use the center of mass. I strongly suggest that you stop using a virtual atom and just use the entire benzene as an argument to the pull code group. I have had difficulties with slightly more complicated setups of this type. Ok, now I'm using only the center of mass of the molecules, no virtual sites. 2. In test2.jpg, the system without pbc shows a flat PMF after the cut-off -- exactly what one would expect. The pbc system shows continued interaction -- again what I would expect. So there is nothing actually all that strange here. One would not expect to see such a drastic difference in a high dielectric such as water, but in vacuum I suspect that this is expected. Alright! In fact the well of both PMFs are not so different. 3. Please clarify what your cutoff was. I don't see a cut-off listed in your .mdp options and leaving this to the default of 1.0 nm is a bad idea because it can lead to confusion a times like this. I might assume that it was 0.7 nm based on test2.jpg, but then see the point #3 below. Apesar de eu nao ter incluido o valor do cutoff na mensagem anterior eu usei 1.2 nm Although I have not included the cutoff value in previous message I used it as 1.2 nm. 4a. I have no idea what -DPOSRES is actually doing for you since I can't see your topology. A ideia de usar POSRES se referia ao emprego dos sitios virtuais. Assim eu restringia a distancia das moleculas atraves da restricao do sitios virtuais sobre seus centros. The idea of using POSRES is referred to the employment of the virtual sites. So I restricted the distance of molecules by restricting virtual sites on their centers. 4b. Are you sure that pull_dim = N N Y is really what you want? Sometimes one wants to average over X and Y, but I am not sure that you do in this case. I want to separate the two molecules from one another so that the displacement is restricted to the z axis. I can be wrong, but I think to do it in water, using PBC, I should use the components distance (N N Y ) with direction geometry to get a pulling in a direction z! Please correct me if it is wrong. 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you? Here they are worthless, because I have not used the option cylinder. I should have removed these options from the original message. ### More minor notes: 5. regarding test1.jpg: a PMF is correct to an additive constant, meaning that you can shift two PMFs relative to one another. These 2 PMFs are therefore less different than they appear in your compaison plot, but they do differ in the slope between 1.0 - 2.0 nm. This is probably just a convergence issue and you will always need to do tests like this. Surely. 6. regarding histo.png: can you confirm that the few very short gaussians are due to less sampling in a few windows? In any event, the overlap looks good. Yes, there were two histograms whose simulations had crashed for some reason. It was corrected. ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br 4. PMF in vacuum and pull direction (chris.ne...@utoronto.ca) Message: 4 Date: Tue, 08 Jun 2010 12:14:34 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum and pull direction To: gmx-users@gromacs.org Message-ID: 20100608121434.u6rhqhz400gc8...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear Eudes: This is better, but I'm afraid that I'm going to have to insist on getting everything I asked for. Please see my previous message. Chris. -- original message -- Dear Chris, I'm so sorry for surperficial email. You are correct because in the previous message I forgot to mention that now the simulation was performed in water (naturally with PBC). The main parameters of the simulation are given below. As I said, I wish to keep the displacement of the pulled molecule at the z-axis, but I'm not getting with this protocol. For the vacuum I followed the tips you gave me earlier and had success! Thanks eef title = Umbrella pulling simulation integrator = sd dt = 0.002 nsteps = 300 constraint_algorithm = lincs constraints = all-bonds nstlist = 5 ns_type = simple rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = Cut-off Tcoupl = V-rescale
[gmx-users] Re: PMF in vacuum (chris.ne...@utoronto.ca)
Hello Chris, thanks for your attention. I'm sending you some links to some tests I performed. As I said you will notice that depending on the parameter used my simulation shows PMF profiles quite different. Especially what concerns to the difference between the use or not of the PBC. https://sites.google.com/site/fileti/files/test1.jpg https://sites.google.com/site/fileti/files/test2.jpg https://sites.google.com/site/fileti/files/histo.png I have constructed two very similar topologies (ben-a.itp and ben-b.itp) where I put a virtual site in the center of benzene. This sites were restrained to keep my molecules fixed distance desired. The basic details of the simulations are given below:1000 define = -DPOSRES integrator = sd tinit= 0 dt = 0.002 nsteps = 500 or 50 comm-mode= angular nstcomm = 1 comm-grps= System bd-fric = 1 ld-seed = 1993 nstlist = 5 ns_type = simple pbc = no or xyz periodic_molecules = no rlist= 0 coulombtype = Cut-off vdw-type = Cut-off rvdw = 0 DispCorr = no Tcoupl = Nose-Hoover tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 constraints = all-bonds constraint_algorithm = lincs ; COM PULLING pull = umbrella pull_geometry= distance pull_dim = N N Y pull_r1 = 1 pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = BENa pull_weights0= pull_pbcatom0= 0 pull_group1 = BENb pull_weights1= pull_pbcatom1= 0 pull_vec1= 0 0 1 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1700 or ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br Dear Eudes: Can you please elaborate on your description? What .mdp options are you using? What exactly do your curves look like (you can post pictures to photobucket or some other online service and link them here)? If you suspect that you are doing something wrong, then we need to understand exactly what you are doing and exactly what you are seeing in order to help. Chris. -- original message -- Hi gmx-users, I'm trying to simulate a umbrella sampling PMF between two benzene molecules in vacuum. My protocol is working fine, my histograms have good overlap and the curves I have got are quite reasonable. However I have noticed that some options in my .mdp file can significantly change the depth of the well. Also the curves can not go to zero at long distances. For example, if I use PBC I get a reasonably good value for the minimum of the PMF but from a certain separation it starts to increase slightly in a linear fashion instead of going to zero. On the other hand, if I make pbc = no, I get an acceptable curve, with the PMF going to zero, but with the minimum too high. Someone could give me any tips on the best set of parameters to calculate this PMF in a vacuum? bests eef -- 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] PMF in vacuum
Hi gmx-users, I'm trying to simulate a umbrella sampling PMF between two benzene molecules in vacuum. My protocol is working fine, my histograms have good overlap and the curves I have got are quite reasonable. However I have noticed that some options in my .mdp file can significantly change the depth of the well. Also the curves can not go to zero at long distances. For example, if I use PBC I get a reasonably good value for the minimum of the PMF but from a certain separation it starts to increase slightly in a linear fashion instead of going to zero. On the other hand, if I make pbc = no, I get an acceptable curve, with the PMF going to zero, but with the minimum too high. Someone could give me any tips on the best set of parameters to calculate this PMF in a vacuum? bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- 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] Restraints of COM
Hello everybody, I have two benzene molecules and I want to restrain them only by their center of mass. The conversation below (between Shirts and Spoel) gave me some ideas but still I couldnt solve the problem. In particular I'm not seeing any way to create this user group, nor how to calculate its center of mass. Could someone give me a hand with that? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- 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] Restraints of COM 2
Hello everybody, I have two benzene molecules and I want to restrain them only by their center of mass. The conversation below (between Shirts and Spoel) gave me some ideas but still I couldnt solve the problem. In particular I'm not seeing any way to create this user group, nor how to calculate its center of mass. Could someone give me a hand with that? On Sun, 2004-01-25 at 04:00, Michael Shirts wrote: Hello, all- So, supposing I had a protein, and wanted to restrain a ligand by attaching it with a spring to some point that wasn't actually an atom -- say it was the center of geometry of a number of atoms around the binding pocket, so that it's a point that redefines itself at each step of the simulation. 1) Is this possible to do using either the position restraint or distance restraint tools in GROMACS? 2) If not, how might one modify the code to put this in? If this is dynamic, like the centre of mass of a group, you might add something using a user group. Compute the center of mass of your user group and call the position restraint routine. The good thing (TM) is that you don't have to program any I/O. Thanks, Michael Shirts Stanford University. -- David. David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- 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] LJ(SR), positive for water
Hello everybody, anyone could help me and understand why the LJ energy is positive for SOL-SOL interactions? The same is not true for LJ energy between benzene (BEN-BEN) and acetonitrile (ACN-ACN). In my opinion it should be negative considering the analytical form LJ potential. Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 BEN-BEN0.0e+00 -2.05557e+030.0e+000.0e+00 ACN-ACN -2.86051e+04 -1.65342e+030.0e+000.0e+00 SOL-SOL -4.75057e+047.45543e+030.0e+000.0e+00 Thanks eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- 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] Angle between normal of rings at same molecule
Dear gmx-users, I have a molecule with two rings and would like to calculate the angle between the normal vector of these rings. Anyone have idea of how this can be done? eef __ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- 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] Decoupling of Coul. and LJ separately in free energy calculation
Dear GMX users, it is recommended the use of two-step procedure for decoupling the solute from the solvent in hydration free energy calculation: first decreasing the charges in the solute, without soft core, and after that, the same procedure is used for the LJ interactions. In version Gromacs 4, how can I do this by using the options couple-moltype(lambda0,lambda1,intramol)? I'm unsure about the use of these options for this purpose. Thanks eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- 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] PBC screw
Hello, grompp 4.0.5 gave me the following error message. ERROR: invalid enum 'full' for variable pbc, using 'xyz' Next time use one of: 'xyz' 'no' 'xy' 'screw' Could someone tell me what does the screw option? I cant find it into paper and online manual, as well as at the gmx-list. bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- 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] Enthapy of vaporization for aromatics
Hello gmx users. I have tried to calculate the enthalpy of vaporization of toluene liquid, which is about 38kJ/mol (exp. value) using the OPLS-UA model (7 sites). I generated the toluene topology adapting a template provided by PRODRG. I have obtained acceptable value for density and structure of the liquid, but for the enthalpy the value is much lower than expected; 18kJ/mol. I know there are subtleties in the treatment of aromatic systems. At Gmx users list I found some tips (see for example http://oldwww.gromacs.org/pipermail/gmx-developers/2009-January/002965.html), but still I can not solve the problem. I already tried numerous ways to circumvent this problem and none worked well. It seems to me the problem may lie in the definition of the dihedrals. Below is the topology that I have used and the main simulation parameters used. If someone can help me I would be very grateful. Bests eef toluene.itp [ moleculetype ] ; Name nrexcl TOL 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_067 1 TOL CH310.000 15.0350 2 opls_076 1 TOL CB 10.000 12.0110 3 opls_075 1 TOL CD 10.000 13.0190 4 opls_075 1 TOL CD 10.000 13.0190 5 opls_075 1 TOL CD 10.000 13.0190 6 opls_075 1 TOL CD 10.000 13.0190 7 opls_075 1 TOL CD 10.000 13.0190 [ bonds ] ; ai aj fuc0, c1, ... 1 2 10.153334720.00.153334720.0 ; CH3 CB 2 3 10.141418400.00.141418400.0 ; CB CD 2 7 10.141418400.00.141418400.0 ; CB CD 3 4 10.141418400.00.141418400.0 ; CD CD 4 5 10.141418400.00.141418400.0 ; CD CD 5 6 10.141418400.00.141418400.0 ; CD CD 6 7 10.141418400.00.141418400.0 ; CD CD [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 1120.0 418.4120.0 418.4 ; CH3 CB CD 1 2 7 1120.0 418.4120.0 418.4 ; CH3 CB CD 3 2 7 1120.0 418.4120.0 418.4 ; CD CB CD 2 3 4 1120.0 418.4120.0 418.4 ; CB CD CD 3 4 5 1120.0 418.4120.0 418.4 ; CD CD CD 4 5 6 1120.0 418.4120.0 418.4 ; CD CD CD 5 6 7 1120.0 418.4120.0 418.4 ; CD CD CD 2 7 6 1120.0 418.4120.0 418.4 ; CB CD CD [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 2 7 3 1 2 0.0 1673.6 ; imp CB CD CD CH3 2 3 4 5 1180.0 12.9704 2 ; imp CB CD CD CD 3 4 5 6 1180.0 12.9704 2 ; imp CD CD CD CD 4 5 6 7 1180.0 12.9704 2 ; imp CD CD CD CD 5 6 7 2 1180.0 12.9704 2 ; imp CD CD CD CB 6 7 2 3 1180.0 12.9704 2 ; imp CD CD CB CD 7 2 3 4 1180.0 12.9704 2 ; imp CD CB CD CD toluene.mdp integrator = md nstlist = 5 ns_type = grid pbc = xyz rlist= 1.2 domain-decomposition = no coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1.2 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.2 DispCorr = EnerPres table-extension = 1 energygrp_table = fourierspacing = 0.12 Tcoupl = berendsen tc-grps = System tau_t= 0.1 ref_t= 300 Pcoupl = No Pcoupltype = isotropic tau_p= 1 compressibility = 5.0e-5 ref_p= 1.1 constraints = none constraint-algorithm = Lincs unconstrained-start = no energygrp_excl = toluene.gro PRODRG COORDS 7 1TOL CH3 1 0.159 -0.143 -0.050 1TOL CB 2 0.154 -0.227 0.078 1TOL CD 3 0.224 -0.349 0.084 1TOL CD 4 0.219 -0.426 0.203 1TOL CD 5 0.145 -0.379 0.313 1TOL CD 6 0.075 -0.256 0.308 1TOL CD 7 0.080 -0.180 0.189 0.51300 0.51300 0.51300 ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
[gmx-users] Re: Normal of the benzene and z axis.
Thanks for the reply. But I have tried use g_sorient tool and I could not see what the sequence of index give me a normal vector of the molecule of benzene. There another tool for this analysis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br wrote: Dear gmx users;How can I calculate the angle distribution forthe angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br ___ 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] Re: Re: Normal of the benzene and z axis.
Dear David, thanks for the reply. In fact 3 carbons can provide me the normal vector of the molecule. But according to manual, g_sorient considers the angle formed by the triple 1 2 3, as the vector that goes from 2 to the midpoint of 1 and 3 (which is the plan of the molecule). So how can I to build a index file for g_sorient to plot the normal vector? Sorry if the question is obvious and I can't to see. Bests ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 Message: 5 Date: Wed, 3 Jun 2009 09:08:43 -0300 From: Eudes Fileti fil...@ufabc.edu.br Subject: [gmx-users] Re: Normal of the benzene and z axis. To: gmx-users@gromacs.org Message-ID: 65e289a20906030508y708e2633rddba6dc6c8f16...@mail.gmail.com Content-Type: text/plain; charset=windows-1252 Thanks for the reply. But I have tried use g_sorient tool and I could not see what the sequence of index give me a normal vector of the molecule of benzene. There another tool for this analysis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br wrote: Dear gmx users;How can I calculate the angle distribution forthe angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/31b76231/attachment-0001.html -- Eudes Fileti wrote: Thanks for the reply. But I have tried use g_sorient tool and I could not see what the sequence of index give me a normal vector of the molecule of benzene. three carbons in the ring. There another tool for this analysis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br mailto:fil...@ufabc.edu.br wrote: Dear gmx users; How can I calculate the angle distribution for the angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br ___ 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] Normal of the benzene and z axis.
Dear gmx users;How can I calculate the angle distribution forthe angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br ___ 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] RDF in GMX 4
Hello, everyone, in earlier versions of the Gromacs the option to calculate rdf between center of mass (com-com) was not implemented. Is this option implemented in version 4.0? If no, someone would have suggestion to calculate the RDF com-com for liquid benzene? thanks EEF ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 skype: eefileti http://fileti.ufabc.edu.br ___ 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] RE: RE: RDF in GMX 4 (Justin)
Thanks for reply Justin. I had already read this part of the manual but I can´t understood it well. How can I take account the mentioned input file run? Would it be a kind of index file? Could you provide me an example? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 skype: eefileti http://fileti.ufabc.edu.br ___ 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] Hydrogen bonds from interface - gOH(z)
Hi everyone, I am working with water in interface with air and I would examine how the hydrogen bonds vary with the distance from the interface. Something like that ( http://pubs.acs.org/appl/literatum/publisher/achs/journals/production/langd5/2009/langd5.2009.25.issue-3/la803324x/images/large/la-2008-03324x_0005.jpeg) However, I am not getting any GMX-tool to perform this analysis. Coul anybody help me to calculated this? bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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] Re: Softcores: sc-power = 1 or 2 ? again (Berk and Justin)
Hello Berk and Justin. Thanks for the help. In fact I was not using hardcore for electrostatic interactions and also had a silly error in my topology. I fix everything and now is working perfectly, without the giant peak near lambda = 0. Bests ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ On Wed, Mar 18, 2009 at 11:44 AM, Eudes Fileti fil...@ufabc.edu.br wrote: Berk Hello, thank you for your attention. My system has 24 hydroxyl groups, and in ethanol, there should be more than 20 solute-solvent hydrogen bonds being erased simultaneously (not to mention the possible intramolecular HB's). I did the simulation using the following protocol: 1) I made disappear the electrostatic interactions turning off the charges (by 200ps), 2) At the sequence I made disappear the LJ interactions (for more 200ps) 3) Finally I performed a run of 0.5ns. Do you think I should extend further the time of the simulations? This will solve the huge peak at lambda = 0? One more thing. Sorry, but so far I can not understood the reason for not to use sc-power=2, which in this case can reduce dramatically the errors associated with the integral of dG/dlambda. ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)
Berk Hello, thank you for your attention. My system has 24 hydroxyl groups, and in ethanol, there should be more than 20 solute-solvent hydrogen bonds being erased simultaneously (not to mention the possible intramolecular HB's). I did the simulation using the following protocol: 1) I made disappear the electrostatic interactions turning off the charges (by 200ps), 2) At the sequence I made disappear the LJ interactions (for more 200ps) 3) Finally I performed a run of 0.5ns. Do you think I should extend further the time of the simulations? This will solve the huge peak at lambda = 0? One more thing. Sorry, but so far I can not understood the reason for not to use sc-power=2, which in this case can reduce dramatically the errors associated with the integral of dG/dlambda. ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ On Wed, Mar 18, 2009 at 8:00 AM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.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. RE: Softcores: sc-power = 1 or 2 ? again (Eudes Fileti) 2. RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess) -- Message: 1 Date: Tue, 17 Mar 2009 23:15:52 -0300 From: Eudes Fileti fil...@ufabc.edu.br Subject: RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again To: gmx-users@gromacs.org Message-ID: 65e289a20903171915jd34087epa77c0d0908af9...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello Berk, I have tried to calculate the free energy of transfer for a polyhydroxylated (from benzene to ethanol). The Dg/dlambda plot, for both, benzene and ethanol shows a very high and narrow peak near lambda=0. In the case of ethanol is worse due to the solute-solvent hydrogen bonds. I performed two sets of simulations, one for sc-power=1 and another for sc-power=2. For sc-power=1 I got a peak much higher than for sc-power=2, and therefore the integration in this case (sc-power=1) could lead me to a much greater error. (please see figure http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer2.jpg) In both cases (ethanol and benzene) the curves coincide for values of lambda beyond 0.4. That is the why of my original question. Not in this case is justified use sc-power=2? Have you any tips on how to ensure the accuracy of calculation of Delta_G in this case? Bests eef Message: 3 Date: Tue, 17 Mar 2009 15:49:12 +0100 From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] Softcores: sc-power = 1 ou 2 ? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: col113-w468577c913d7e1af9301238e...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Hi, Never (unless you want to reproduce old simulations). Berk Date: Tue, 17 Mar 2009 10:50:48 -0300 From: fil...@ufabc.edu.br To: gmx-users@gromacs.org Subject: [gmx-users] Softcores: sc-power = 1 ou 2 ? Hello, I have a doubt regarding the use of soft-core. When the use of sc-power = 2 is more recommended than sc-power = 1?eef___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090317/f3b6882b/attachment-0001.html -- Message: 2 Date: Wed, 18 Mar 2009 11:07:02 +0100 From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: col113-w565a4b17f474c3559010a08e...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Hi, The shape of the dgdl curves also depends a lot on alpha (and sc-sigma). From your plots I am guessing that you are doing LJ and electrostatics at the same time. This always results in high peaks when
[gmx-users] Softcores: sc-power = 1 ou 2 ?
Hello, I have a doubt regarding the use of soft-core. When the use of sc-power = 2 is more recommended than sc-power = 1? eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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] Softcores: sc-power = 1 or 2 ? again
Hello Berk, I have tried to calculate the free energy of transfer for a polyhydroxylated (from benzene to ethanol). The Dg/dlambda plot, for both, benzene and ethanol shows a very high and narrow peak near lambda=0. In the case of ethanol is worse due to the solute-solvent hydrogen bonds. I performed two sets of simulations, one for sc-power=1 and another for sc-power=2. For sc-power=1 I got a peak much higher than for sc-power=2, and therefore the integration in this case (sc-power=1) could lead me to a much greater error. (please see figure http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer2.jpg) In both cases (ethanol and benzene) the curves coincide for values of lambda beyond 0.4. That is the why of my original question. Not in this case is justified use sc-power=2? Have you any tips on how to ensure the accuracy of calculation of Delta_G in this case? Bests eef Message: 3 Date: Tue, 17 Mar 2009 15:49:12 +0100 From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] Softcores: sc-power = 1 ou 2 ? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: col113-w468577c913d7e1af9301238e...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Hi, Never (unless you want to reproduce old simulations). Berk Date: Tue, 17 Mar 2009 10:50:48 -0300 From: fil...@ufabc.edu.br To: gmx-users@gromacs.org Subject: [gmx-users] Softcores: sc-power = 1 ou 2 ? Hello, I have a doubt regarding the use of soft-core. When the use of sc-power = 2 is more recommended than sc-power = 1?eef___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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] Diffusion coefficients ( Exp X Simul )
David thanks for the reply, it was that such references I was looking for. One more little thing. These models describe poorly only the D of the water or for the other solvents too? Bests eef Message: 6 Date: Tue, 03 Mar 2009 22:41:04 +0100 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Diffusion coefficients ( Exp X Simul ) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49ada3f0.4090...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: Hello, someone could suggest me references which discusses the difficulty of obtaining values for diffusion coefficients in agreement to the experimental values? For water that is well known, but I do not know of any reference that discusses this topic You mean that models do not reproduce D? You could have a look at JCP 119 pp. 7308-7317 (2003) and references therein. There is quite a lot of literature. Thanks eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 59, Issue 31 * ___ 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] Diffusion coefficients ( Exp X Simul )
Hello, someone could suggest me references which discusses the difficulty of obtaining values for diffusion coefficients in agreement to the experimental values? For water that is well known, but I do not know of any reference that discusses this topic Thanks eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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] CO2 Linear triatomic - topology problem
Hi gmx-users, I am trying to build a CO2 topology. Because CO2 is a triatomic linear molecule there is a discontinuity in the potential for the angle of 180 degrees, so I must use virtual sites to circumvent the problem. I have create my topology (gave below) from arguments I read in the forum (http://www.gromacs.org/pipermail/gmx-users/2003-February/004394.html) and for which I was a brief summary, also below. But when I run the simulation I get the following error message. virtual site D1 (Res CO2) has non-zero mass 21.90158 I understand and agree that the message, but what I do not understand is, why the topology for CO2 gives this error, while that for acetonitrile (below) does not. Someboy could help me find the error? Thanks eef *** My CO2 Topology *** [ moleculetype ] ; name nrexcl CO22 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 D1 1 CO2D110. 21.90158 2 D2 1 CO2D210. 21.90158 3 O1 CO2OC1 -0.3256 0.0 4 C1 CO2CO10.6512 0.0 5 O1 CO2OC1 -0.3256 0.0 [ constraints ] ; ai aj funct b0 1 2 1 0.2000 [ dummies2 ] ; aiajak funct a 3 1 2 1 0.0170 4 1 2 1 0.1000 5 1 2 1 0.2170 [ exclusions ] 3 4 5 4 5 3 5 4 3 ;*** *** *** From forum *** ;For acetonitrile ;The com of MeCN I get from: ;M = sum(mi) ;rcom = sum(mi*ri)/M ;The inertia tensor of a linear molecule is: ; [Ia 0 0] ;I = [0 Ia 0] with Ia=sum(mi(ri-rcom)^2) ; [0 0 0] ;Now I have to choose to masses m1 and m2 with r1 and r2 relativ to the com: ;The distance R between m1 and m2 can be chosen freely: ;R = r1 - r2 ;There are three conditions to be satisfied: ;M = m1 + m2 ;m1*r1 + m2*r2 = 0 ;m1*r1^2 + m2*r2^2 = Ia ;Using these 4 eqn I can calculate the four unknows. ; ; ;The correct Me-N-distance from the reference i cited is 0.263nm. ;The distance R between D1(m1) and D2(m2) is in priciple free to choose. ;only if you choose it shorter than r(Me-N) the quadratic equation ;you find for the first unknown paramter to define becomes undefined: ; ; M*R +- sqr(M^2R^2-4MIa) ;r1 = --- ; 2M ; ;I got two solutions for r1. Calculating r2=r1-R will give you the ;negative of the other solution. I have chosen the solution ;that makes physical sense to me: ; ;D1--Me---+-C--D2---N ; ^ ; | ; com ;You have to consider that m(D1)m(D2). Hence the above config makes more ;sense than the other mathematical solution: ; ; Me-D2+-C---N-D1 ; ; *** *** ;*** Forum Acetonitrile Topology *** [ atomtypes ] ;type mass chargeptype c6c12 D1 9.49031 0.000 D 0.0 0.0 D2 31.56239 0.000 D 0.0 0.0 MeAN 0.0 0.000 A 0.90571E-02 0.26212E-04 ; (*) CAN 0.0 0.000 A 0.51454E-02 0.12167E-04 ; (*) NAN 0.0 0.000 A 0.26955E-02 0.28943E-05 ; (*) [ moleculetype ] ; name nrexcl Acetonitril2 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 D1 1 MeCND1AN10.000 9.49031 2 D2 1 MeCND2AN10.000 31.56239 3 MeAN 1 MeCNC3AN10.206 0.0 4 CAN 1 MeCNC4AN10.247 0.0 5 NAN 1 MeCNN5AN1 -0.453 0.0 [ constraints ] ; ai aj funct b0 1 2 1 0.26300 [ dummies2 ] ; aiajak funct a 3 1 2 1 0.2652197 4 1 2 1 0.8203527 5 1 2 1 1.2652197 [ exclusions ] 3 4 5 4 5 3 5 4 3 ;(*) E.Guardia, Mol. Simul. 26, 2001, 2878; ;A rigid two mass system with the same mom. of inertia ;as MeCN is used to provide a linear molecule. Me, C and ;N are defined as dummies relativ to D1 and D2. ; eof --- *** *** ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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] Free energy of transfer with accuracy
Hello David, thanks for the reply! I am simulating the free energy of transfer of the C60, from ethanol to benzene. The softcore parameters, I used the are the same values of Tieleman et.al. (nature nanotechnology, 3, 363). At figure, each curve refers to a different solvent; one of them for ethanol and another for benzene. For lambda=0 I have the Coulomb and LJ parameters turn on and for lambda=1, turn off. I have found a large difference when simulating my system using sc_power=2. See in this link ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-scpower.jpg ) the comparison between plots from sc_power=1 and sc_power=2 for solute in benzene. Near 0 and 1, I believe that problem cancels out at difference, as can seen at ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg ) . Then the main problem, in my view, is in the intermediate region, where the plot presents a deep (-500 units) and noise minimum. Observe that in lambda=0, sc_power=2 reduce largely the derivative, but the critical region, one that makes the difference in calculation of the transfer free energy, remains the same, ie, the derivative still oscilates a lot and is not smooth. Are you believe that changing the value of alpha from 0.47 to 0.50 can resolve this? Please, ask me more details if you need. Thanks again. eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ -- Message: 4 Date: Thu, 11 Dec 2008 07:24:26 -0600 From: David Mobley [EMAIL PROTECTED] Subject: Re: [gmx-users] Free energy of transfer with accuracy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Hi, Hi gmx-users, I have tried to calculate the free energy of transfer of a solute between two solvents by thermodynamic integration. However, the dgdl plot I have obtained is not smooth enough to ensure accuracy. I have used a non homogeneous spacing for lambda. The first is from 0.0 to 0.4 (dl=0.04), the second is from 0.405 to 0.48 (dl=0.005) and the third is from 0.48 to 1 (dl=0.04). Overall, I was performed 40 simulations. As can be seen in the figure ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg ), there is a large fluctuation in the region that goes from 0.40 to 0.48. Each simulation was carried out by 0.5ns preceded by 0.15ns of equilibration. I am using soft-core whose parameters are: ; Free energy control stuff free_energy = yes init_lambda = 0.00 delta_lambda = 0 sc_alpha = 1.3 sc-power = 1.0 (for this I also used 2). sc-sigma = 0.47 In the example of the link sc-power=1, but I re-did the calculations with sc-power=1 and I found the same behavior (although the format of the plot was a little different). Can you suggest me a way to calculate this free energy difference with accuracy? The perturbation free energy method could give better results? Thank you EEF This does look alarming. I would make a couple comments here: 1) Soft core parameters can be fairly sensitive. Michael Shirts and I have both looked at these independently and we find that sc-power = 1.0 with an alpha of 0.5 is typically substantially better than most other options. Even alpha = 0.47 or 0.53 can be much worse than alpha = 0.5. Your dV/dlambda curve looks to me like your soft core values are far from ideal and that you are seeing a huge peak near lambda = 0 for this reason. 2) Am I interpreting your e-mail correctly that lambda = 0 corresponds to one solvent, and lambda = 1 corresponds to another? If so, I am unclear on how exactly you're doing the transformation and could use more detail on how you've set this up. A more straightforward (and easier?) way to do this would be to transfer the solute to vacuum from each solvent and then take the difference in the vacuum transfer free energies. Please clarify which you're doing so we can help better. David Mobley, Ph.D. Assistant Professor of Chemistry University of New Orleans New Orleans, LA 70148 [EMAIL PROTECTED] Office 504-280-6445 Fax 504-280-6860 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Free energy of transfer with accuracy
Hello David, I use to follow the rule 2 always. However in all of these simulations, the carbon atoms have no charge. Well, I will do what you suggest: Perform simulations with: ; Free energy control stuff free_energy = yes init_lambda = 0.00 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.5 Also I will simulate longer times (say 1.5ns) for lambdas ranging between 0.40 and 0.45 for 0005. But first I would want to know two things. 1) The parameter sc-sigma of 0.5 is reasonable? How this parameter affects the shape of dvdl plot? You performed tests about it? I found little about it in the forum. 2) In my tests, I realized that, simply changing the electrostatic interactions treatment (cut-off or PME), a large difference it was found at hydration free energy. With cutoff I have found 12.2kJ/mol while with PME, 24.0kJ/mol. The accepted value must be around 20kJ/mol). This to me was somewhat surprising, because, as mentioned above, C60 does not have charge, so that effect should be minimized or zero. In any case I assign it to the electrostatic of the solvent. I suppose the PME result is more reliable, it's ok? Do you know some work that explore the effect of the electrostatic of the solvent on the solvation free energy? Thank you eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ Subject: Re: [gmx-users] Free energy of transfer with accuracy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Eudes, On Thu, Dec 11, 2008 at 8:27 AM, Eudes Fileti [EMAIL PROTECTED] wrote: Hello David, thanks for the reply! I am simulating the free energy of transfer of the C60, from ethanol to benzene. The softcore parameters, I used the are the same values of Tieleman et.al. (nature nanotechnology, 3, 363). At figure, each curve refers to a different solvent; one of them for ethanol and another for benzene. For lambda=0 I have the Coulomb and LJ parameters turn on and for lambda=1, turn off. I have found a large difference when simulating my system using sc_power=2. See in this link ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-scpower.jpg ) the comparison between plots from sc_power=1 and sc_power=2 for solute in benzene. Near 0 and 1, I believe that problem cancels out at difference, as can seen at ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg ) . Then the main problem, in my view, is in the intermediate region, where the plot presents a deep (-500 units) and noise minimum. Observe that in lambda=0, sc_power=2 reduce largely the derivative, but the critical region, one that makes the difference in calculation of the transfer free energy, remains the same, ie, the derivative still oscilates a lot and is not smooth. Are you believe that changing the value of alpha from 0.47 to 0.50 can resolve this? OK, there are several issues here. 1) The noisy minimum in dV/dlambda 2) The overall shape of dV/dlambda 3) Other potential problems On (1), the noisiness of the minimum you refer to really means there are convergence problems for some reason -- probably correlation times are particularly long there. This may be helped by using the soft core parameters I mention, but I am not sure. See item #3. On (2), in general, the overall shape of dV/dlambda seems to be smoothest and best behaved with the particular soft core parameters I mention. We did a lot of testing on this (i.e., many values of alpha at each of several sc-power values). On (3), there are other thing that can go wrong when using soft core. See http://www.alchemistry.org/wiki/index.php/Best_Practices for some discussion, and see rule #2 in particular. If you have any partial charges on atoms in your C60 this could be a potential source of error and noise. Also, if your C60 is hollow, I can imagine that it might exclude solvent atoms from the inside, in which case you are going to have a big convergence issue as solvent begins to interpenetrate with the C60, which may lead to noise problems when this starts to happen, whatever soft core functional form you use. This just means you will need to run longer simulations in this regime. Anyway, long story short, I suggest two things: (a) Make sure you turn off partial charges on C60 (without using soft core) before turning off the LJ using soft core, and (b) use the soft core functional form I suggest. David Please, ask me more details if you need. Thanks again. eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC
[gmx-users] Free energy of transfer with accuracy
Hi gmx-users, I have tried to calculate the free energy of transfer of a solute between two solvents by thermodynamic integration. However, the dgdl plot I have obtained is not smooth enough to ensure accuracy. I have used a non homogeneous spacing for lambda. The first is from 0.0 to 0.4 (dl=0.04), the second is from 0.405 to 0.48 (dl=0.005) and the third is from 0.48 to 1 (dl=0.04). Overall, I was performed 40 simulations. As can be seen in the figure ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg ), there is a large fluctuation in the region that goes from 0.40 to 0.48. Each simulation was carried out by 0.5ns preceded by 0.15ns of equilibration. I am using soft-core whose parameters are: ; Free energy control stuff free_energy = yes init_lambda = 0.00 delta_lambda = 0 sc_alpha = 1.3 sc-power = 1.0 (for this I also used 2). sc-sigma = 0.47 In the example of the link sc-power=1, but I re-did the calculations with sc-power=1 and I found the same behavior (although the format of the plot was a little different). Can you suggest me a way to calculate this free energy difference with accuracy? The perturbation free energy method could give better results? Thank you EEF ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How long should I run a free energy simulation
Hi all,I am performing some free energy test calculations for benzene in water. How long should I run a simulation so that I get reliable result on my test? Thanks eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Constraints - PMF - Different Molecules (Mark Abraham/Arthur Roberts)
Dear Mark and Arthur, thank you for your reply. I did what you suggest me and almost everything worked. I created a topology with the two molecules without bonded parameters between them and put constrains on two of its atoms. I did a minimization and a simulation (md integrator). It worked perfectly. But when I tried to perform the calculation to free energy using the options below, the simulation failed. Setting free-energy no the simulation works again. Do you have any suggestions? Bests eef ; Free energy control stuff free-energy = yes init-lambda = 1.0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 Error Message: Back Off! I just backed up dgdl.xvg to ./#dgdl.xvg.9# starting mdrun 'C60 - PMF' 3 steps, 60.0 ps. Back Off! I just backed up traj.trr to ./#traj.trr.18# step 0Warning: 1-4 interaction between 5 and 28 at distance 1.398 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Arthur Roberts wrote: Dear Eudes, You need to technically make it 1 big molecule. As long as there are no bonds specified between molecule A and B. The big molecule will behave as if there are two molecules in it. I do it to dock small molecules to proteins. That's a good description, Arthur, thanks. 1) Combine molecules A and B into a big structure file (i.e. pdb or gro). 2) Edit this file, so that they are the same chain. 3) run pdb2gmx 4) Change all the residue names to MOL and change Protein_A to MOL in the top and pdb files. 5) Make sure that there is no bonds between molecule A and B in the top file. There probably won't be, but it is good to check anyway. 5) run grompp to check this file to see if it is acceptable to gromacs. 6) add distance restraints after the improper dihedrals. If you put it anywhere else, it will not work. That contradicts the description of the topology file format on (e.g.) page 109 of the GROMACS 4 manual - starting with GROMACS 3.1.3 all directives at the parameter level can be used multiple times and there are no restrictions on the order, except that an atom type must be defined before it can be used in other definitions. 7) run grompp again to check this file to see if it is acceptable to gromacs Other advise: 1) I would roughly dock the molecules together, so that you don't have to have such a large water box. 2) I would experiment with force constants and time constants for the distance restraints. A useful article is: Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Constraints - PMF - Different Molecules
Hi Mark, sorry, but could you be more specific whenyou say Combine the topologies? Was not it what I had done early? Thank you eef The error you report is potentially of the everyday http://wiki.gromacs.org/index.php/blowing_up variety. See http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off First, get your separated-molecules topology and initial structure working for basic MD. Then combine the topologies. Only then introduce your next layer of complexity with constraints-restraints. Then worry about PMF stuff. Even for experts, troubleshooting where something went wrong is easier if you only make one lot of changes at a time before testing for correctness. ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Constraints - PMF - Different Molecules (Mark Abraham)
Hello Mark, thanks for your attention. I had already made some attempts setting the two molecules in the same block (as suggested in the forum) but I had no success. I tried to use restraints and constraints and but run always fails. Please I am sending my .mdp and .top files as well as the error message that I getting. Note, there is no bonded parameters molecules between two molecules. Can you help me to solve this problem? .mdp file cpp = integrator = md tinit = 0.0 dt = 0.01 nsteps = 1 nstcomm = 1 nstxout = 1000 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 # with 1000 we get 1/1000 == 10 (+ original, t=0) frames xtc_precision = 1000 nstlist = 10 energygrps = ns_type = grid rlist = 0.9 coulombtype = cut-off rcoulomb= 0.9 rvdw= 0.9 Tcoupl = Berendsen tc_grps = system ref_t = 90 tau_t = 0.2 Pcoupl = No tau_p = 1.0 compressibility = 1e-4 ref_p = 1.0 gen_vel = yes gen_temp= 90 gen_seed= 173529 free-energy = yes init-lambda = 0.96 delta-lambda = -.64 # in order to get down to .32 nm with 1 steps #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl BEN 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_075 1BEN C1 1 0 13.019 ; qtot 0 2 opls_075 1BEN C2 2 0 13.019 ; qtot 0 3 opls_075 1BEN C3 3 0 13.019 ; qtot 0 4 opls_075 1BEN C4 4 0 13.019 ; qtot 0 5 opls_075 1BEN C5 5 0 13.019 ; qtot 0 6 opls_075 1BEN C6 6 0 13.019 ; qtot 0 7 opls_075 2BEN C1 7 0 13.019 ; qtot 0 8 opls_075 2BEN C2 8 0 13.019 ; qtot 0 9 opls_075 2BEN C3 9 0 13.019 ; qtot 0 10 opls_075 2BEN C4 10 0 13.019 ; qtot 0 11 opls_075 2BEN C5 11 0 13.019 ; qtot 0 12 opls_075 2BEN C6 12 0 13.019 ; qtot 0 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 1 6 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 2 3 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 3 4 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 4 5 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 5 6 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 7 8 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 712 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 8 9 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 910 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 1011 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 1112 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 [ pairs ] ; aiaj functc0c1c2c3 1 4 1 2 5 1 3 6 1 710 1 811 1 912 1 [ angles ] ; aiajak functc0c1c2 c3 2 1 6 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 1 2 3 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 2 3 4 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 3 4 5 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 4 5 6 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 1 6 5 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 8 712 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 7 8 9 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 8 910 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 91011 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 101112 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 71211 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 6 1 2 3 3 1.80e+02 5.00e+00 3.00e+00
[gmx-users] Re: Free energy - Hydrogen bond solute-solvent - Ethanol as an example.
Hello all I have tried to reproduce the hydration free energy (TI) of the ethanol from Hess and van der Vegt (JPCB, 110, 17616). The value I have obtained is around 20kJ/mol while the reference value is -20.1kJ/mol (if not the sign ...). If someone can help me find the mistake I would be very grateful. Below are the simulation details. I followed the protocol of the paper, Berk: I used 47 lambda values (because of hydrogen bonds between solute-solvent) (dense near lambda=0 and between 0.46 and 0.72). I am turning off the LJ and Coulomb terms separately. Softcore (alpha = 0.5, power = 1), OPLS-AA Timestep = 2fs, sd = integrator, PME constrained = none trajectories = 40ps (NVT) (I know that is small, but I looking for qualitative results) after 20ps of equilibration (NPT). I have found a value of -4.8kJ/mol for the DeltaG(vacuum) (relative to mutate the ethanol to dummy in vacuum). My dv/dl curve (for DeltaG(water) is below. Should I expect this form? I think there are many high positive values. The numerical integration is 15.9kJ. So, DG(hyd) = DG(wat) - DG(vac) = 15.9 - (-4.8) = 20.7kJ I believe that this protocol is OK (but I want to confirm that). @title dG/d\8l\4 @xaxis label Time (ps) @yaxis label dG/d\8l\4 (kJ mol\S-1\N [\8l\4]\S-1\N) @TYPE xy 0.000 4.431073e+02 0.005 3.660083e+02 0.010 2.987275e+02 0.015 2.023206e+02 0.000 4.431073e+02 0.005 3.660083e+02 0.010 2.987275e+02 0.015 2.023206e+02 0.020 1.905198e+02 0.030 1.086573e+02 0.040 4.217960e+01 0.050 4.101856e+01 0.060 2.314358e+01 0.070 2.223774e+01 0.080 2.669019e+01 0.090 1.696131e+01 0.100 6.089735e+00 0.110 9.569030e+00 0.120 1.505562e+01 0.130 2.785974e+00 0.140 2.440906e+00 0.150 3.050463e+00 0.160 8.578429e-01 0.200 3.577259e+00 0.240 -3.532969e+00 0.280 5.842623e+00 0.320 7.912565e+00 0.360 9.322502e+00 0.400 -2.930754e+00 0.440 2.797944e+00 0.460 5.113900e+00 0.480 -3.919665e+00 0.500 -9.000282e+00 0.520 -7.636168e+00 0.540 -7.574299e+00 0.560 -2.144124e+01 0.580 -6.618514e+00 0.600 -2.755925e+01 0.620 -1.491331e+01 0.640 -2.541398e+01 0.660 -5.213154e+01 0.680 -2.364612e+01 0.700 -2.535817e+01 0.720 -7.767502e+00 0.760 -1.096362e+01 0.800 1.136031e+01 0.840 2.883933e+01 0.880 4.465743e+01 0.920 5.461566e+01 0.960 6.882000e+01 1.000 7.673736e+01 -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Free energy - Hydrogen bond solute-solvent - Ethanol as an example.
Hello to all I have tried to reproduce the hydration free energy (TI) of the ethanol from Hess and van der Vegt (JPCB, 110, 17616). The value I have obtained is around 20kJ/mol while the reference value is -20.1kJ/mol (if not the sign ...). If someone can help me find the mistake I would be very grateful. Below are the simulation details. I followed the protocol of the paper, Berk: I used 47 lambda values (because of hydrogen bonds between solute-solvent) (dense near lambda=0 and between 0.46 and 0.72). I am turning off the LJ and Coulomb terms separately. Softcore (alpha = 0.5, power = 1), OPLS-AA Timestep = 2fs, sd = integrator, PME constrained = none trajectories = 40ps (NVT) (I know that is small, but I looking for qualitative results) after 20ps of equilibration (NPT). I have found a value of -4.8kJ/mol for the DeltaG(vacuum) (relative to mutate the ethanol to dummy in vacuum). My dv/dl curve (for DeltaG(water) is below. Should I expect this form? I think there are many high positive values. The numerical integration is 15.9kJ. So, DG(hyd) = DG(wat) - DG(vac) = 15.9 - (-4.8) = 20.7kJ I believe that this protocol is OK (but I want to confirm that). @title dG/d\8l\4 @xaxis label Time (ps) @yaxis label dG/d\8l\4 (kJ mol\S-1\N [\8l\4]\S-1\N) @TYPE xy 0.000 4.431073e+02 0.005 3.660083e+02 0.010 2.987275e+02 0.015 2.023206e+02 0.000 4.431073e+02 0.005 3.660083e+02 0.010 2.987275e+02 0.015 2.023206e+02 0.020 1.905198e+02 0.030 1.086573e+02 0.040 4.217960e+01 0.050 4.101856e+01 0.060 2.314358e+01 0.070 2.223774e+01 0.080 2.669019e+01 0.090 1.696131e+01 0.100 6.089735e+00 0.110 9.569030e+00 0.120 1.505562e+01 0.130 2.785974e+00 0.140 2.440906e+00 0.150 3.050463e+00 0.160 8.578429e-01 0.200 3.577259e+00 0.240 -3.532969e+00 0.280 5.842623e+00 0.320 7.912565e+00 0.360 9.322502e+00 0.400 -2.930754e+00 0.440 2.797944e+00 0.460 5.113900e+00 0.480 -3.919665e+00 0.500 -9.000282e+00 0.520 -7.636168e+00 0.540 -7.574299e+00 0.560 -2.144124e+01 0.580 -6.618514e+00 0.600 -2.755925e+01 0.620 -1.491331e+01 0.640 -2.541398e+01 0.660 -5.213154e+01 0.680 -2.364612e+01 0.700 -2.535817e+01 0.720 -7.767502e+00 0.760 -1.096362e+01 0.800 1.136031e+01 0.840 2.883933e+01 0.880 4.465743e+01 0.920 5.461566e+01 0.960 6.882000e+01 1.000 7.673736e+01 -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Infinite system PBC and Bonded Interaction
Hello all Now I'm getting a different error. Suddenly, a water molecule fragments itself and the simulation stops. And when I do a complete simulation (with a number of steps immediately before the crash) it presents many inconsistent shifts. I search the forum for a solution and the tips were always to update the Gromacs. I am using version 3.3.3 and errors still occur. Someone would have any suggestions? Thanks eef On Fri, Apr 25, 2008 at 10:31 AM, Eudes Fileti [EMAIL PROTECTED] wrote: Dear Mark, thank you for your reply and suggestion. I was forgetting the follow detail: Be absolutely sure that the terminal carbon atoms are sharing a bond in the topology file Now everything is working perfectly! Thanks again eef Message: 1 Date: Fri, 25 Apr 2008 09:14:00 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Infinite system PBC and Bonded Interaction To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: I am simulating a infinite graphene sheet in water. The expected is that the system it is infinite in xy plane. But after the simulation I note that the edges of the box (in particular the graphene) are not replicables, i. e., it do not match with its images. I suspect that I may be wrong in using any option mdp file I got the same result for both full and xyz for option pbd. What have I to do to my system be infinitely replicated, with all its bonded interaction matching? There's some advice here for an analogous problem that might help - http://wiki.gromacs.org/index.php/Carbon_Nanotube Mark ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ http://cromo.ufabc.edu.br/%7Efileti/ -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Infinite system PBC and Bonded Interaction
Dear Mark, thank you for your reply and suggestion. I was forgetting the follow detail: Be absolutely sure that the terminal carbon atoms are sharing a bond in the topology file Now everything is working perfectly! Thanks again eef Message: 1 Date: Fri, 25 Apr 2008 09:14:00 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Infinite system PBC and Bonded Interaction To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: I am simulating a infinite graphene sheet in water. The expected is that the system it is infinite in xy plane. But after the simulation I note that the edges of the box (in particular the graphene) are not replicables, i. e., it do not match with its images. I suspect that I may be wrong in using any option mdp file I got the same result for both full and xyz for option pbd. What have I to do to my system be infinitely replicated, with all its bonded interaction matching? There's some advice here for an analogous problem that might help - http://wiki.gromacs.org/index.php/Carbon_Nanotube Mark ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Infinite system PBC and Bonded Interaction
I am simulating a infinite graphene sheet in water. The expected is that the system it is infinite in xy plane. But after the simulation I note that the edges of the box (in particular the graphene) are not replicables, i. e., it do not match with its images. I suspect that I may be wrong in using any option mdp file I got the same result for both full and xyz for option pbd. What have I to do to my system be infinitely replicated, with all its bonded interaction matching? -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Tools for axial symmetry
Dear colleagues I have made simulation of infinite nanotubes in solvent environment. However I can not use the usual tools of the GROMACS to analyze my simulation (as g_rdf, trajorder, etc) due to axial symmetry (cylindrical). Problem that I need to solve are the calculation of rdf (taking as reference the axis of the nanotube, not the COM) and also the analysis of the number of molecules into the first solvation shell. Have anybody some suggestion of standalone program or GROMACS tools for help me? Thanks eef -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Protonate and OPLS
Dear gmx users The tool protonate also works for the OPLS force field or only for GMX? I tried and I did not obtain sucess! Bests eef -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How can I add hydrogen?
Dear gmx users I run a simulation of the liquid of acetonitrila (OPLS-UA) and I need of the configurations with explicit hydrogen atoms. Somebody could help me add the H atoms to configurations? eef -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 43, Issue 21
Dear Florian, The tool protonate also works for the OPLS force field or only for GMX? I tried and I did not obtain sucess! Bests eef To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Dear gmx users I run a simulation of the liquid of acetonitrila (OPLS-UA) and I need of the configurations with explicit hydrogen atoms. Somebody could help me add the H atoms to configurations? eef -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ http://cromo.ufabc.edu.br/%7Efileti/ From: Florian Haberl [EMAIL PROTECTED] Subject: Re: [gmx-users] How can I add hydrogen? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=utf-8 Hi, On Tuesday, 6. November 2007 18:13, Eudes Fileti wrote: Dear gmx users I run a simulation of the liquid of acetonitrila (OPLS-UA) and I need of the configurations with explicit hydrogen atoms. Somebody could help me add the H atoms to configurations? eef try protonate -h Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) âˆ' 9131 âˆ' 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Potential energy positive. Can be?
Dear Mark, thank you for your reply. For equilibration of the system, firstly I generated a ordinated lattice of 10x10x10 molecules. After, I carried out successive minimization runs (with STEEP and L-BFGS) up to the system to reach the convergence for these methods and in the sequence I performed simulations totalizing 300ps, in ensemble NVT. (Could you suggest something more appropriate?) I believe that if I start from a configuration with molecules randomly distributed I would get better results than a ordinated configuration. I have created the potential for the toluene from of the potential of the benzene and and it seemed the sufficiently reasonable, compared to others potentials from literature. And about this, would you a topology or a equilibrated box for the toluene? Thanks again. eef Message: 4 Date: Thu, 16 Aug 2007 08:35:26 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Potential energy positive. Can be? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: Hi gmx users, I have tried to simulate a box with 1000 molecules of toluene and I always have obtained a positive value for the potential energy. I have used three different models of potential (with and without 14 interactions) and all of them provides a positive value for energy. I must be falling in some error or making some wrong analysis but I do not know what. Below I put the average values that I got from the simulations that I made. If somebody will be able to help me, I will be grateful! How are you equilibrating these structures? For how long are you doing so? Two questions about these results: # Why are so larger the values for LJ-14? Because they're from atoms near each other. You don't just turn them on and off to suit the phase of the moon, you need to choose whether they're included according to how the force field was developed and is intended to be used. Search GROMACS manual for OPLS to see what is recommended, and/or read the original OPLS paper (reference in the GROMACS manual). # How can I compose the potential energy from the components? Would not be U = LJ + Coul + bond + ang + dihed ? And LJ-14? You add them up. Every energy term that isn't kinetic or total is a potential energy. Mark ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Potential energy positive. Can be?
Dear Mark, Thank you for the link. It was useful. I have choosen the volume using the editiconf by setting the experimental density for toluene. In fact, my potential can be wrong. So, I asked you if you would have a topology or an equilibrated box for the toluene, since this could be very useful to me. (but my text was not understandable, sorry). Thanks so much. eef Message: 5 Date: Fri, 17 Aug 2007 01:16:36 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Potential energy positive. Can be? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: Dear Mark, thank you for your reply. For equilibration of the system, firstly I generated a ordinated lattice of 10x10x10 molecules. After, I carried out successive minimization runs (with STEEP and L-BFGS) up to the system to reach the convergence for these methods and in the sequence I performed simulations totalizing 300ps, in ensemble NVT. (Could you suggest something more appropriate?) Check out http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation, in particular, how did you choose your volume? (and thus density and pressure?) Is this reasonable? I believe that if I start from a configuration with molecules randomly distributed I would get better results than a ordinated configuration. As soon as you're generating random velocities, it won't matter at all whether the starting configuration was ordered or not. After 10ps or less you won't be able to see any ordering. I have created the potential for the toluene from of the potential of the benzene and and it seemed the sufficiently reasonable, compared to others potentials from literature. Looking reasonable is not a sufficient criterion if you want to publish these results. You're simulating a complex balance of different interactions and our intuition is poorly-trained to see what is good or not in this context. The only measure of quality is the ability to reproduce (experimental) observables. Hence my point about using an existing forcefield in exactly the same way, and not making something up. The fact that you are getting positive energies suggests that at least on of the above issues is a significant problem for your system. And about this, would you a topology or a equilibrated box for the toluene? I don't understand you. Mark -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Potential energy positive. Can be?
Hi gmx users, I have tried to simulate a box with 1000 molecules of toluene and I always have obtained a positive value for the potential energy. I have used three different models of potential (with and without 14 interactions) and all of them provides a positive value for energy. I must be falling in some error or making some wrong analysis but I do not know what. Below I put the average values that I got from the simulations that I made. If somebody will be able to help me, I will be grateful! Bests eef Two questions about these results: # Why are so larger the values for LJ-14? # How can I compose the potential energy from the components? Would not be U = LJ + Coul + bond + ang + dihed ? And LJ-14? USING OPLS-UA with 14 interactions == ### == A V E R A G E S == ### == Energies (kJ/mol) Bond Angle Improper Dih. LJ-14 Coulomb-14 1.74553e+042.86624e+031.04333e+046.20512e+040.0e+00 LJ (SR) Disper. corr. Coulomb (SR) PotentialKinetic En. -3.90255e+04 -4.73494e+032.98090e+014.90753e+042.62518e+04 Total EnergyTemperature Pressure (bar) 7.53271e+043.00743e+02 -3.32933e+00 USING GMX with 14 interactions == ### == A V E R A G E S == ### == Energies (kJ/mol) Bond Angle Improper Dih. LJ-14 Coulomb-14 1.75692e+043.90052e+038.64676e+035.45622e+04 -1.01334e+02 LJ (SR) Disper. corr. Coulomb (SR) PotentialKinetic En. -4.84750e+04 -2.16220e+03 -8.82568e+013.38519e+042.62111e+04 Total EnergyTemperature Pressure (bar) 6.00630e+043.00276e+021.23474e+00 USING OPLS-AA with 14 interactions == ### == A V E R A G E S == ### == Energies (kJ/mol) Bond Angle LJ-14 Coulomb-14LJ (SR) 2.63123e+042.60679e+044.35409e+04 -1.94043e+04 -4.08125e+04 Disper. corr. Coulomb (SR) Coul. recip. PotentialKinetic En. -1.39923e+037.83183e+028.19773e+034.32861e+045.65749e+04 Total EnergyTemperature Pressure (bar) 9.98610e+043.02436e+022.24669e+03 USING OPLS-AA without 14 interactions == ### == A V E R A G E S == ### == Energies (kJ/mol) Bond AngleLJ (SR) Disper. corr. Coulomb (SR) 2.02244e+042.43199e+04 -4.04650e+04 -1.39923e+031.24955e+03 Coul. recip. PotentialKinetic En. Total EnergyTemperature 8.38794e+031.23176e+045.56793e+046.79968e+042.97648e+02 Pressure (bar) 1.73270e+03 -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 34, Issue 4
Dear gmx users, I have attempted to run the calculation of vacf. I always receive a message Killed when my analysis arrives in one specific frame. I already looked at my trajectory with gmxcheck and it seems ok. I also looked for in the forum for similar problem and I did find anything. What it could be this message of error? Thanks eef ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ 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] g_sorient to ethanol
Good ideia Dr Hess! Only more thing. I would have to rerun the simulation to make the C atoms of ethanol 1 and 2 (since my C atoms have index 1 and 5)? Or there is another more practical way of change the index of atoms? eef ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ 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] g_sorient. Only for water?
Dear GMX users The tool g_sorient is applicable only when the solvent is the water? I have attemped to apply it for the case of solvation in ethanol and I am not obtaining an appropriate vector for the calculation of the angle. In fact, it woul be very nice if I can make the C=C bond of ethanol like a vector. Some suggestion? eef ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ 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] g_sorient. Again.
Dear Berk, Thank you for the reply. Actually my problem is not related to the analysis of bonds but of angles. Specifically, I am interested in the distribution of the angle I between the C=C bond of etanol with a plan of my solute molecule. It also would be interesting to analyze as this angle varies with the distance, since I believe that solute modifies significantly the local structure of the solvent. Could you suggest me a procedure or tool? Bests eef ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ 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] Re: gmx-users Digest, Vol 33, Issue 70
Fatal error: Something wrong with contents of index file. you may need to add the -type flag, run g_sgangle -h -- David. Sorry David, but seems that the g_sgangle utility has not this option. eef ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ 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] Re: gmx-users Digest, Vol 33, Issue 69
I am trying to calculate the angle between two plans. For this I created an index file with all triples of atoms related to each plan. Thus I would get the angle between the normal of these plans. To get the index file I used: mk_angndx -s topol.tpr -n angle.ndx To calculate the angles I used g_sgangle -f traj.xtc -n angle.ndx -s topo.tpr -oa sg_angle.xvg However I obtained the following error. Anyone could say me as to overcome this? thanks eef Reading file term.tpr, VERSION 3.3 (single precision) Group 0 (Theta=108.0_334.72) has 180 elements Group 1 (Theta=120.0_585.76) has 360 elements Group 2 (Theta=110.7_313.8) has 15000 elements Group 3 (Theta=107.8_276.144) has 12000 elements Group 4 (Theta=109.5_418.4) has 3000 elements Group 5 (Theta=108.5_460.24) has 3000 elements Group 6 (Theta=109.5_292.88) has 6000 elements Select a group: 0 4 Selected 0: 'Theta=108.0_334.72' Select a group: Selected 4: 'Theta=109.5_418.4' Group Theta=108.0_334.72 contains the following atoms: Atomname 0: C3 Atomname 1: C1 Atomname 2: C9 Atomname 3: C4 Atomname 4: C2 Atomname 5: C10 Atomname 6: C1 Atomname 7: C3 Atomname 8: C5 ... Atomname 177: C40 Atomname 178: C60 Atomname 179: C45 Group Theta=108.0_334.72 contains the following atoms: Atomname 0: C3 Atomname 1: C1 Atomname 2: C9 Atomname 3: C4 Atomname 4: C2 Atomname 5: C10 Atomname 6: C1 Atomname 177: C40 Atomname 178: C60 Atomname 179: C45 Careful: distance only makes sense in some situations. Reading frame 0 time0.000 Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2# --- Program g_sgangle, VERSION 3.3 Source code file: gmx_sgangle.c, line: 127 Fatal error: Something wrong with contents of index file. --- It's So Fast It's Slow (F. Black) ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ 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] Calculation of the angle between planes: g_sgangle
Dear gmx users I am trying to calculate the angle between two planes. For this I created an index file with all triples of atoms related to each plane. Thus I would get the angle between the normal of these planes. To get the index file I used: mk_angndx -s topol.tpr -n angle.ndx To calculate the angles I used g_sgangle -f traj.xtc -n angle.ndx -s topo.tpr -oa sg_angle.xvg However I obtained the following error. Anyone could say me as to overcome this? thanks eef Reading file term.tpr, VERSION 3.3 (single precision) Group 0 (Theta=108.0_334.72) has 180 elements Group 1 (Theta=120.0_585.76) has 360 elements Group 2 (Theta=110.7_313.8) has 15000 elements Group 3 (Theta=107.8_276.144) has 12000 elements Group 4 (Theta=109.5_418.4) has 3000 elements Group 5 (Theta=108.5_460.24) has 3000 elements Group 6 (Theta=109.5_292.88) has 6000 elements Select a group: 0 4 Selected 0: 'Theta=108.0_334.72' Select a group: Selected 4: 'Theta=109.5_418.4' Group Theta=108.0_334.72 contains the following atoms: Atomname 0: C3 Atomname 1: C1 Atomname 2: C9 Atomname 3: C4 Atomname 4: C2 Atomname 5: C10 Atomname 6: C1 Atomname 7: C3 Atomname 8: C5 ... Atomname 177: C40 Atomname 178: C60 Atomname 179: C45 Group Theta=108.0_334.72 contains the following atoms: Atomname 0: C3 Atomname 1: C1 Atomname 2: C9 Atomname 3: C4 Atomname 4: C2 Atomname 5: C10 Atomname 6: C1 Atomname 177: C40 Atomname 178: C60 Atomname 179: C45 Careful: distance only makes sense in some situations. Reading frame 0 time0.000 Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2# --- Program g_sgangle, VERSION 3.3 Source code file: gmx_sgangle.c, line: 127 Fatal error: Something wrong with contents of index file. --- It's So Fast It's Slow (F. Black) ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ 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] How can I generate a FCC unit cell?
Hi gmx-users, I need to generate a FCC unit cell (in fact a face centered cubic lattice) in order to produce a nanocristal. I would like to know if is possible to make this using directly GROMACS. In affirmative case, as I can make it? Thanks in advance ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ 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] Buckingham model for liquid of water
Dear gmx-ersI have attemped to use the potential of Buckingham to simulate the water liquid. However I did not find papers that present the parameters of the potential. Actually I found a paper that mixed parameters LJ (O...O) and Buckingham (O-H, O-O and H...O). Can anyone let me know if there is a optmized set parameters for the water with this potential ?Thankseef-- __Eudes Eterno FiletiCentro de Ciência Naturais e Humanas Universidade Federal do ABCRua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ 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] Internal coordinates to the topology
Dear gmx-userI have a crystalline cell with 150 atoms. Somebody would know to say me as to generate the pairs (bond), triples (angles) and quaternios (dihedral) for the topology?Is there a good program to do this? For smaller molecules the Gaussian works finebut in this case its fails. I already used PRODRG but I have not sucess...Thanks in advanceeef__Eudes Eterno FiletiCentro de Ciência Naturais e Humanas Universidade Federal do ABCRua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ 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] Uncorrelated configurations
Dear Gmx Users I have one trajectory of 800ps. I need extract of this trajectory, only the uncorrelated (statistically independent) configurations. So I need know how many ps separates two consecutive configuratios. Which procedure I can use for this analysis? Thanks eef __Eudes Eterno FiletiCentro de Ciência Naturais e HumanasUniversidade Federal do ABCRua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ 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] Re: gmx-users Digest, Vol 28, Issue 42
Dear David Actually I posted my doubt in Vol 28, Issue 38. There I detailed more. Anyway, my system is 1 C60 molecule in 1000 ethanol molecules. As said, I need of structures that do not remember the previous one, i.e. that are structural and statistically not correlated. For this, up to now, I have attemped to use the autocorrelation function of the energy and the block averaging process, but I am still uncertain about the results. An interesting option it could be the analyzis of van Hove function, but I dont kwow how calculate them. Bests eef __Eudes Eterno FiletiCentro de Ciência Naturais e HumanasUniversidade Federal do ABCRua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ 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] Benzene and normal modes
Dear GMX usersI think that this question already is old but Could anyone tell me as I could simulate a benzene molecule fixed by its center (at the center of the box) but with its vibration normal modes free?__Eudes Eterno FiletiCentro de Ciência Naturais e Humanas Universidade Federal do ABCRua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ 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] Problems with the Dihedral of the Ethanol
Dear gmx users I have attemped to simulate a box of ethanol in normal conditions of temperature and pressure. I reproduced very well some literature data (as g(r)) however I had problems to reproduce the angulardistribution function for the dihedral (C-C-O-H). This angle must have a peak in 180 degrees and two lesser (and symmetrical) peaks in 60 and 300 degrees (as shows the figure 1 of this link http://cbio.mskcc.org/~leonor/jpcb97.pdf ).However my distribution presents a maximum in 100 degrees with two (but not symmetrical) peaks the left. I already made almost everything: I used both, dihedral GROMACS and Ryckaert-Bellemans, I applied almost all the avaliables parameters (eg in ffoplsaabon.itp), I set nrexcl 2, 3, 4, 5, I remade the simulation several times in with differents conditions, but always I found the same pattern. Somebody already had some experience like that? If it had, could you give me a insight? Bellow I give my top file.Thank you in advance.eef ;; File 'etanol.top' was generated; By user: fileti (1000); On host: linux; At date: Sat Jul 15 16:41:25 2006;; This is your topology file ; Out Of Register Space (Ugh) (Vi);; Include forcefield parameters#include ffoplsaa.itp[ moleculetype ]; Name nrexclETH 2[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_135 1 EtOH CB 1 -0.18 12.011 ; qtot -0.18 2 opls_140 1 EtOH HB1 1 0.06 1.008 ; qtot -0.12 3 opls_140 1 EtOH HB2 1 0.06 1.008 ; qtot -0.06 4 opls_140 1 EtOH HB3 1 0.06 1.008 ; qtot 0 5 opls_157 1 EtOH CA 2 0.145 12.011 ; qtot 0.145 6 opls_140 1 EtOH HA1 2 0.06 1.008 ; qtot 0.205 7 opls_140 1 EtOH HA2 2 0.06 1.008 ; qtot 0.265 8 opls_154 1 EtOH OH 2 - 0.683 15.9994 ; qtot -0.418 9 opls_155 1 EtOH HO 2 0.418 1.008 ; qtot 0[ bonds ]; ai aj funct c0 c1 1 2 1 0.10800 284512.0 1 3 1 0.10800 284512.0 1 4 1 0.10800 284512.0 1 5 1 0.14040 392459.2 5 6 1 0.10800 307105.6 5 7 1 0.10800 307105.6 5 8 1 0.13640 376560.0 8 9 1 0.09450 462750.4 [ angles ]; ai aj ak funct c0 c1 2 1 3 1 107.800 276.144 2 1 4 1 107.800 276.144 2 1 5 1 107.800 276.144 3 1 4 1 107.800 276.144 3 1 5 1 110.700 313.800 4 1 5 1 110.700 313.800 1 5 6 1 109.500 292.880 1 5 7 1 109.500 292.880 1 5 8 1 109.500 418.400 6 5 7 1 107.800 276.144 6 5 8 1 115.000 334.720 7 5 8 1 108.000 585.760 5 8 9 1 109.000 292.880 [ dihedrals ]; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 5 6 3 1.67360 -1.67360 0.0 0.0 0.0 0.0 2 1 5 7 3 1.67360 -1.67360 0.0 0.0 0.0 0.0 2 1 5 8 3 0.97905 2.93716 0.0 -3.91622 0.0 0.0 3 1 5 6 3 1.67360 -1.67360 0.0 0.0 0.0 0.0 3 1 5 7 3 1.67360 -1.67360 0.0 0.0 0.0 0.0 3 1 5 8 3 0.97905 2.93716 0.0 -3.91622 0.0 0.0 4 1 5 6 3 1.67360 -1.67360 0.0 0.0 0.0 0.0 4 1 5 7 3 1.67360 -1.67360 0.0 0.0 0.0 0.0 4 1 5 8 3 0.97905 2.93716 0.0 -3.91622 0.0 0.0 1 5 8 9 3 26.15000 -3.13800 -23.01200 0.0 0.0 0.0 6 5 8 9 3 0.94140 2.82420 0.0 -3.76560 0.0 0.0 7 5 8 9 3 0.94140 2.82420 0.0 -3.76560 0.0 0.0__Eudes Eterno Fileti Centro de Ciência Naturais e HumanasUniversidade Federal do ABCRua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ 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] Label of the atoms in ffoplsaabon.itp
Dear Gmx users:I am a new user and I have some questionsSomebody could say me what it means the index at atoms in the ffoplsaabon.itp file (a fragment of fileis gave bellow). Some are obvious (OH, is oxygen bonden to hydrogen and HO is a hydrogen bonded to oxygen) but definitively I dont know what type of bond makes the carbon atoms like C_2, C_3 or C *.I cant find this issue at manual so forgive me for the basic question.Thank youeef; Some esoteric OPLS atomtypes are not freely available (or depreciated). ; Interaction types involving these have been commented out.[ bondtypes ]; i j func b0 kb OW HW 1 0.09572 502080.0 ; For TIP4F Water - wlj 1/98 OW LP 1 0.01750 753120.0 ; -idem- C* HC 1 0.10800 284512.0 ; C C3 1 0.15220 265265.6 ; END C_2 C3 1 0.15220 265265.6 ; END C_3 C3 1 0.15220 265265.6 ; END C CA 1 0.14900 334720.0 ; wlj 8/97 C_2 CA 1 0.14900 334720.0 ; wlj 8/97 C_3 CA 1 0.14900 334720.0 ; wlj 8/97 C CB 1 0.14190 374049.6 ; GUA C_2 CB 1 0.14190 374049.6 ; GUA C_3 CB 1 0.14190 374049.6 ; GUA C CM 1 0.14440 343088.0 ; THY C_2 CM 1 0.14440 343088.0 ; THY C_3 CM 1 0.14440 343088.0 ; THY C CS 1 0.14900 334720.0 ; C_2 CS 1 0.14900 334720.0 ; C_3 CS 1 0.14900 334720.0 ; C CT 1 0.15220 265265.6 ; C_2 CT 1 0.15220 265265.6 ; C_3 CT 1 0.15220 265265.6 ; C CT_2 1 0.15220 265265.6 ; AA Calpha C_3 CT_2 1 0.15220 265265.6 ; AA C-term NO ON 1 0.12250 460240.0 ; wlj nitro CS CW 1 0.13670 456892.8 ; wj/nm CS CS 1 0.14240 392459.2 ; -idem- CS CB 1 0.14240 392459.2 ; -idem- CS HA 1 0.10800 307105.6 ; -idem- CU NB 1 0.13200 343088.0 ; -idem- CU CA 1 0.14210 392459.2 ; -idem- CU HA 1 0.10800 307105.6 ; -idem- NA NB 1 0.13490 334720.0 ; -idem- OS NB 1 0.13990 386601.6 ; -idem- OS CR 1 0.13570 386601.6 ; -idem- C3 C3 1 0.15260 217568.0 ; Ethane C! C! 1 0.14600 322168.0 ; wlj C! CS 1 0.14600 322168.0 ; wlj__Eudes Eterno FiletiCentro de Ciência Naturais e HumanasUniversidade Federal do ABC Rua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ 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
