[gmx-users] principal moments of ellipsoid
Hi, I want to study the shape change of a macromolecule which seems like a ellipsoid. So, I need obtain the three principal moments of the molecules. Is the command of g_gyrate helpful for me? The sum of the three principal moments should be equal to the Rg^2. However, I used the command g_gyrate -f traj.gro -s nvt.tpr -n anly.ndx -o shape.xvg -p obtain the Rg and other three qualities. It seems that the sum of the last three qualities is not equal to the Rg^2. Is there something wrong? -- wade -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] principal moments of ellipsoid
Not R_x, R_y, and R_z. What I want to obtain are the three three principal moments of the ellipsoidal macromolecule. They are different quantities. 2011/5/10 Erik Marklund er...@xray.bmc.uu.se Mark Abraham skrev 2011-05-10 12.31: On 10/05/2011 8:23 PM, lammps lammps wrote: Hi, I want to study the shape change of a macromolecule which seems like a ellipsoid. So, I need obtain the three principal moments of the molecules. Is the command of g_gyrate helpful for me? The sum of the three principal moments should be equal to the Rg^2. However, I used the command g_gyrate -f traj.gro -s nvt.tpr -n anly.ndx -o shape.xvg -p obtain the Rg and other three qualities. It seems that the sum of the last three qualities is not equal to the Rg^2. Is there something wrong? Why should that sum equal Rg^2? Mark Shouldn't it be half of that sum? Rg^2 = 1/N Sum([r_k - r]^2), where r are vectors and masses are set to unity for conveniance. If decomposed in orthonormal axes x, y, and z, it yealds Rg^2 = 1/N Sum([x_k-x]^2 + [y_k-y]^2 + [z_k-z]^2). The radius of gyration around e.g. the x-axis is Rg_x^2 = !/N Sum([y_k-y]^2 + [z_k-z_k]^2). Hence Rg^2 = (Rg_x^2+Rg_y^2+Rg_z^2) / 2. That matches the numbers I get from my tests. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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 -- wade -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] principal moments of ellipsoid
Yes, However, what does the data in axis1.dat, axis2.dat, axis3.dat and moi.dat mean? Should I put the center-of-mass of the molecule in the origin when using the g_principal command? It seems that the inertia is calculated relative to the origin. May be my understanding wrong. -- wade -- 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] How to control the temperature when using an electric field?
Hi, I want to use the option of E_x = 1 0.01 0 to add an electric field to the simulated system in NVT ensemble. Because there should exist an no zero velocity of center-of-mass in the x direction. It seems that it is wrong to directly use the nose-hoover to control the temperature. it is also not reasonable to use nstcomm = 1, because the velocity of center-of mass in the x-axis should be kept when runing. So, How to control the temperature? When calcating the temperature in the process of simulations, how to exclude the velocity of center-of-mass of x direction for controling the right T? Thanks in advance. -- wade -- 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] how to write a rtp file for amido amine
Hi everybody, I want to use pdb2gmx command to create a .gro file and a .top file for PAMAM whose repeat unit is amidoamine ( attached ). / ---CH2--CH2--CO-NH-CH2-CH2-N(see the attached figure) \ The atom N have two same branches with --CH2--. I write the rtp file for it as follows: [ atoms ] C1opls_245-0.0501 . [ bonds ] C1-N7 ... C6N7 N7+C1 N7+C1 It seems not work, which gives a wrong top structure. The question is how can I deal with the two branches of N. Any suggestion is appreciated. Thanks in advance. -- wende attachment: amidoamine.jpg-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to write a rtp file for amido amine
Hi Mark, Thanks for your reply. But, I do not know the meaning of the columns in specbonds.dat. I also do not find any information in the manual 4.0. Could you provide something about the specbonds.dat or give some explanations. Thanks in advance. 2010/10/9 Mark Abraham mark.abra...@anu.edu.au - Original Message - From: lammps lammps lammp2fo...@gmail.com Date: Saturday, October 9, 2010 19:27 Subject: [gmx-users] how to write a rtp file for amido amine To: Discussion list for GROMACS users gmx-users@gromacs.org Hi everybody, I want to use pdb2gmx command to create a .gro file and a .top file for PAMAM whose repeat unit is amidoamine ( attached ). / ---CH2--CH2--CO-NH-CH2-CH2-N(see the attached figure) \ The atom N have two same branches with --CH2--. I write the rtp file for it as follows: [ atoms ] C1opls_245-0.0501 . [ bonds ] C1-N7 ... C6N7 N7+C1 N7+C1 It seems not work, which gives a wrong top structure. The question is how can I deal with the two branches of N. Any suggestion is appreciated. pdb2gmx is intended only for work with linear heteropolymers. Any more complex things (e.g. disulfides, branched structures) have to be engineered using the specbonds.dat mechanism. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- wende -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to write a rtp file for amido amine
Thanks for Mark and Justin's help. But I have new questions as follows: CYS SG 1 HEMEFE 2 0.25CYS2HEME 1.residue name A 2.atom name A 3.number of bonds that this atom can form (does the number include the bonds of atom with H atoms?) 4.residue name B 5.atom name B 6.number of bonds that this atom can form 7.the reference length for searching for candidate bonds, the margin is ±10%( It seems the unreasonable length can result in the unexpected bond. does it? ) 8.the new name for residue A ( Why new residue name?) 9.the new name for residue B Thanks again. 2010/10/9 Justin A. Lemkul jalem...@vt.edu lammps lammps wrote: Hi Mark, Thanks for your reply. But, I do not know the meaning of the columns in specbonds.dat. I also do not find any information in the manual 4.0. Could you provide something about the specbonds.dat or give some explanations. http://www.gromacs.org/Documentation/File_Formats/specbond.dat -Justin Thanks in advance. 2010/10/9 Mark Abraham mark.abra...@anu.edu.au mailto: mark.abra...@anu.edu.au - Original Message - From: lammps lammps lammp2fo...@gmail.com mailto:lammp2fo...@gmail.com Date: Saturday, October 9, 2010 19:27 Subject: [gmx-users] how to write a rtp file for amido amine To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi everybody, I want to use pdb2gmx command to create a .gro file and a .top file for PAMAM whose repeat unit is amidoamine ( attached ). / ---CH2--CH2--CO-NH-CH2-CH2-N(see the attached figure) \ The atom N have two same branches with --CH2--. I write the rtp file for it as follows: [ atoms ] C1opls_245-0.0501 . [ bonds ] C1-N7 ... C6N7 N7+C1 N7+C1 It seems not work, which gives a wrong top structure. The question is how can I deal with the two branches of N. Any suggestion is appreciated. pdb2gmx is intended only for work with linear heteropolymers. Any more complex things (e.g. disulfides, branched structures) have to be engineered using the specbonds.dat mechanism. Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- wende -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- wende -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to write a rtp file for amido amine
get it Thanks very much!! 2010/10/10 Justin A. Lemkul jalem...@vt.edu lammps lammps wrote: Thanks for Mark and Justin's help. But I have new questions as follows: CYS SG 1 HEMEFE 2 0.25CYS2HEME 1.residue name A 2.atom name A 3.number of bonds that this atom can form (does the number include the bonds of atom with H atoms?) It should pertain to the number of bonds you want that atom to form, aside from those in the .rtp entry. See the line for HIS NE2, which forms one bond to FE, but certainly forms other bonds to atoms in the HIS residue. 4.residue name B 5.atom name B 6.number of bonds that this atom can form 7.the reference length for searching for candidate bonds, the margin is ą10% ( It seems the unreasonable length can result in the unexpected bond. does it? ) I don't understand your question. If you define a bond at, i.e. 0.1 nm, pdb2gmx will build a bond if the distance between the two atoms is 0.9 - 1.1 nm. An unreasonable bond will only be formed if you provide an unreasonable search distance. 8.the new name for residue A ( Why new residue name?) This isn't always relevant. Note that most of the entries in specbond.dat remain unchanged. The only instances of the residue name changing are related to force field-specific disulfide conventions (i.e., CYS vs. CYS2). -Justin 9.the new name for residue B Thanks again. 2010/10/9 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu lammps lammps wrote: Hi Mark, Thanks for your reply. But, I do not know the meaning of the columns in specbonds.dat. I also do not find any information in the manual 4.0. Could you provide something about the specbonds.dat or give some explanations. http://www.gromacs.org/Documentation/File_Formats/specbond.dat -Justin Thanks in advance. 2010/10/9 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au - Original Message - From: lammps lammps lammp2fo...@gmail.com mailto:lammp2fo...@gmail.com mailto:lammp2fo...@gmail.com mailto:lammp2fo...@gmail.com Date: Saturday, October 9, 2010 19:27 Subject: [gmx-users] how to write a rtp file for amido amine To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi everybody, I want to use pdb2gmx command to create a .gro file and a .top file for PAMAM whose repeat unit is amidoamine ( attached ). / ---CH2--CH2--CO-NH-CH2-CH2-N(see the attached figure) \ The atom N have two same branches with --CH2--. I write the rtp file for it as follows: [ atoms ] C1opls_245-0.0501 . [ bonds ] C1-N7 ... C6N7 N7+C1 N7+C1 It seems not work, which gives a wrong top structure. The question is how can I deal with the two branches of N. Any suggestion is appreciated. pdb2gmx is intended only for work with linear heteropolymers. Any more complex things (e.g. disulfides, branched structures) have to be engineered using the specbonds.dat mechanism. Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- wende -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users
[gmx-users] the total charge of a neutral molecules is not zero
Dear everyone, I use OPLS AA field to deal with a neutral molecules. However, the Total charge is 8.500 e, not zero. Are there other reasons for this problem except giving a wrong parameter due to my carelessness. I can not find the errors. Any suggest is appreciated. Thanks in advance. -- wade -- 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] OPLS-AA force field
Hi everybody, I want to use OPLS-AA force field to do simulation for dendrimer(see the attached files for figure and .pdb). If the pH4.0，the tertiary amines on the dendrimer will be protonated, i.e. (CH2)3-N will be changed to (CH2)3-NH+. Now, I have two questions as follows. 1. How can I use pdb2gmx to get the .gro and .itp? It seems there are not the *residue.* 2. I don't find the suitable force field for the N in (CH2)3-NH+, How can I deal with this? Any suggestion is appreciated. Thanks in advance. -- wende attachment: g2.gif Dendrim.pdb Description: Protein Databank data -- 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] mean force.
Hi everyone, I use umbrella sample and g_wham to get potential of mean force. However, I also want to compute the mean force. How can I deal with this? Can I get it through calculating the average of data in pullf.xvg file? Thanks in advance. Wende -- ;spring point is equal to ref_group0+pull_init+time*pull_rate*pull_vec， pull = Umbrella;umbrella,constraint pull_geometry = Distance;distance ,direction,cylinder,position pull_dim = Y Y Y pull_group0 = DEN1 pull_group1 = DEN2 pull_nstxout = 500 pull_nstfout = 50 pull_init1= 5.7 pull_k1 = 1000 --- # This file was created Thu Feb 4 00:51:24 2010 # by the following command: # mdrun_mpi -rdd 1.4 -s npt.tpr -c npt.gro # # mdrun_mpi is part of G R O M A C S: # # Groningen Machine for Chemical Simulation # @title Pull force @xaxis label Time (ps) @yaxis label Force (kJ/mol/nm) @TYPE xy 0. -28.8555 1.6000 -19.2897 3.2000 -18.59 4.8000 -20.7866 6.4000 -26.1605 8. -42.8572 9.6000 -50.7524 11.2000 -73.9647 12.8000 -74.2521 14.4000 -102.284 16. -96.5184 -- wende -- 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] g_order in GMX4.05
Hello everyone, I use the g_order to get the order parameter of the tails( C1A, C2A, C3A, C4A) of DPPC. The are 100 molecules of DPPC 1. I use the make_ndx -f dppc.trr -n index to produce the index file. a C1A a C2A a C3A a C4A del 0-3 Q_1: Is the method right to produce the index file? Then there only four groups orderly named C1A, C2A, C3A, C4A in the index file. 2. I use the g_order -n index -s npt.tpr ... to get the order parameter. However, there are lots of errors . WARNING: distance between atoms 29777 and 29779 0.3 nm (0.897513). Index file might be corrupt. WARNING: distance between atoms 29789 and 29791 0.3 nm (0.709495). Index file might be corrupt. WARNING: distance between atoms 29801 and 29803 0.3 nm (0.692954). Index file might be corrupt. WARNING: distance between atoms 29813 and 29815 0.3 nm (0.784918). Index file might be corrupt. WARNING: distance between atoms 29825 and 29827 0.3 nm (0.839048). Index file might be corrupt. WARNING: distance between atoms 29837 and 29839 0.3 nm (0.851105). Index file might be corrupt. WARNING: distance between atoms 29849 and 29851 0.3 nm (0.790752). Index file might be corrupt. WARNING: distance between atoms 29861 and 29863 0.3 nm (0.836583). Index file might be corrupt. WARNING: distance between atoms 29873 and 29875 0.3 nm (0.854105). Index file might be corrupt. WARNING: distance between atoms 29885 and 29887 0.3 nm (0.847901). Index file might be corrupt. WARNING: distance between atoms 29897 and 29899 0.3 nm (0.758556). Index file might be corrupt. ... Why? 3. Result Last frame 4 time 240.000 Read trajectory. Printing parameters to file Atom 1 Tensor: x=-0.267416 , y=-0.245994, z=0.51341 Atom 2 Tensor: x=-0.207203 , y=-0.171233, z=0.378436 Back Off! I just backed up order.xvg to ./#order.xvg.1# Back Off! I just backed up deuter.xvg to ./#deuter.xvg.1# gcq#51: The Stingrays Must Be Fat This Year (Red Hot Chili Peppers) [tia...@localhost dppcden5]$ cat order.xvg # This file was created Sun Apr 23 10:10:35 2006 # by the following command: # g_order -f traj.trr -n index.ndx -s npt.tpr -o -e 240 # # g_order is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title Order tensor diagonal elements @xaxis label Atom @yaxis label S @TYPE xy 1 -0.267416 -0.2459940.51341 2 -0.207203 -0.171233 0.378436 [tia...@localhost dppcden5]$ -- wende -- 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] fix a group in truncated octahedron
Sorry for this. Thanks for your kind reply. That is the answer of my question. Actually, I only want to make sure whether the command of energygrp_excl has the ability not to calculate the force in the group. The manual about energygrp_excl seems not talk about how to deal with the force. Maybe, I do not fully understand this command. energygrp excl: Pairs of energy groups for which all non-bonded interactions are excluded. An example: if you have two energy groups Protein and SOL, specifying energygrp excl = Protein Protein SOL SOL would give only the non-bonded interactions between the protein and the solvent. This is especially useful for speeding up energy calculations with mdrun -rerun and for excluding interactions within frozen groups. --- Happy new year. 2009/12/28 chris.ne...@utoronto.ca Hi Wende, please do not double post. If you are unsure if your post got through, you can easily see the list at http://lists.gromacs.org/pipermail/gmx-users/2009-December/date.html. You did not put units beside 40, so I suppose that you mean 40 A, whereas gromacs uses nm. 1. Make a box with one sodium ion and then editconf -c -d 4 -bt dodecahedron. This will give you your box, then you can put your lattice inside it. With properly selected atom in an index file, you could easily do this in one step based on the commands above (plus the index group with a single central atom). 2. This is clearly laid out in the manual under energygrp_excl. You should familiarize yourself with the online .mdp file options at http://manual.gromacs.org/current/online/mdp_opt.html which will help you find such things. Chris. -- original message -- Hi GMX users, I want to fix a group in a truncate octahedron. How can I dealt with the questions below, 1. I hope the box corresponds to an inscribed circle of cubic of size 40*40*40, how to calculate the box vectors? 2. One spherical rigid body consists of face-center cubic lattices is fixed in the center of the box. I do not want to calculate the force and energy between the paritcles of this rigid body, so that no matter how large force between them shoud not blow up the rigid body. How can I do this? Thanks in advance. -- wende -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- wende -- 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] fix a group in truncated octahedron
Hi GMX users, I want to fix a group in a truncate octahedron. How can I dealt with the question below, There is One spherical rigid body consists of face-center cubic lattices fixed in the center of the box. I do not want to calculate the force and energy between the paritcles of this rigid body, so that no matter how large force between them shoud not blow up the rigid body. How can I do this? Thanks in advance. -- wende -- 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] fix a group in truncated octahedron
Hi GMX users, I want to fix a group in a truncate octahedron. How can I dealt with the questions below, 1. I hope the box corresponds to an inscribed circle of cubic of size 40*40*40, how to calculate the box vectors? 2. One spherical rigid body consists of face-center cubic lattices is fixed in the center of the box. I do not want to calculate the force and energy between the paritcles of this rigid body, so that no matter how large force between them shoud not blow up the rigid body. How can I do this? Thanks in advance. -- wende -- 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] fix a group in truncated octahedron
Hi, I want to fix a group in a truncate octahedron. How can I dealt with the questions below, 1. I hope the box corresponds to an inscribed circle of cubic of size 40*40*40, how to calculate the box vectors? 2. One spherical rigid body consists of face-center cubic lattices is fixed in the center of the box. I do not want to calculate the force and energy between the paritcles of this rigid body, so that no matter how large force between them shoud not blow up the rigid body. How can I do this? Thanks in advance. -- wende -- 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] steered MD simulation for calculating the PMF
Hello, I want to use the Steered molecular dynamics simulations to calculate the PMF with Gromacs. How could I write the pull code? Are there some examples? And what files the GMX will create when running the SMD code? Then how to obtain the PMF after full running? Is there any command for this? Thanks in advance. -- wende -- 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] How to calculate the PMF?
Dear all, It is the first time that I use gromacs 4.04 to calculate PMF. I have some question needed to be clarified. 1. ; ; pull code for PMF pull= Unbrella;unbrella,constraint pull_geometry = Distance;distance ,direction,cylinder,position pull_dim = N N Y pull_group0 = DPPC pull_group1 = DEN pull_nstxout= 100 pull_nstfout = 100 pull_init1 = 3.8 pull_k1 = 1000 Is there any relationship between the steps for pull_nstxout and pull_nsfout. Must they be the same( e.g. 100, 100)? How to choose them? 2. It seems that there are only two output file: pullx.xvg and pullf.xvg. Is it right? are there other files for the input of g_wham? 3. What other thing I must take care of for calculation of PMF Thanks in advance. -- wende -- 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] how to obtain the hydrogen bond energy?
Hi, I used the OPLS-AA FF to simulate the PEO and water systems. The are hydrogen bond between PEO and water. I want to obtain the average energy of these dydrogen bond. How can I do? Should I calculate the free energy? Any idea is appreciated. Thanks in advance. -- wende -- 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] reduced units
Dear, I want to do stochastic simulations in the framework of Langevin dynamics using Gromacs with the reduced units. The questions are: 1. How to turn on the reduced units? Is there any parameters for setting? 2. If I use the reduced temperature of 1, should the ref_t in the .mdp file be the 120.2717 ? Right? 3. I create the force field(.itp and .top) within the reduced units myself. Are there any suggestion for avoiding errors? Thanks in advance. -- wende ___ 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] how to create a PEO Residue database
Hi everyone, The structural formula of PEO is CH3-- O- CH2 - CH2 - (O - -CH2 - CH2 )n - O - -CH2 - CH2 - O - CH3 I have obtain all the OPLS-AA FF for PEO from a paper such as atomtypes, bondtypes, angletypes, and dihedraltypes. Then I have a .PDB of PEO. I need a residuce to create .top and .gro. The questions are 1. What is the suitable residuce datebase of PEO I must create myselt for the command pdb2gmx conversing PDB to .top and .gro? 2. If there is a suitable residuce, what file should I change except the ffoplsaa.rtp? Any suggestion is appreciated. Thanks in advance. -- wende ___ 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] PEO and OPLS-AA FF in gmx
Hi, I want to simulate a PEO chain in water using OPLs-AA FF in Gromacs. I have created a .PDB file using Material Studio, but I seems that the pdb2gmx can not dealt with it because of the error Residue 'xx' not found in residue topology database The question is how can I obtain the .top and .gro file in the framework of OPLS-AA FF. Any suggestion is appreciated. Thanks in advance. -- wende ___ 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] question about g_rdf
Dear everyone, I use the command (g_rdf -f traj.trr -s md.tpr -o rdf_12.xvg -sq sq_12.xvg -b 1000 -bin 0.01 -cut 1.2 -grid 0.05 ) to calculate the RDF There are two questions: Question_1: Why should we do the three times selections[ the red line], Reading file md.tpr, VERSION 4.0.4 (single precision) Reading file md.tpr, VERSION 4.0.4 (single precision) Select 1 group【the first time, what aim is this selection? 】 Opening library file /home/tianwd/soft/gromacs 4//share/gromacs/top/aminoacids.dat Group 0 ( System) has 5240 elements Group 1 ( SOL) has 5216 elements Group 2 ( CL-) has12 elements Group 3 ( NA+) has12 elements Select a group: 3 Selected 3: 'NA+' trn version: GMX_trn_file (single precision) Reading frame1500 time 3000.000 Last frame 1500 time 3000.000 Reading file md.tpr, VERSION 4.0.4 (single precision) Select a reference group and 1 group【the second time must select two groups 】 Opening library file /home/tianwd/soft/gromacs4//share/gromacs/top/aminoacids.dat Group 0 ( System) has 5240 elements Group 1 ( SOL) has 5216 elements Group 2 ( CL-) has12 elements Group 3 ( NA+) has12 elements Select a group: 1 Selected 1: 'SOL' Select a group: 3 Selected 3: 'NA+' Reading frame 600 time 1200.000 Q_2: What is the reasons for the following error? Select 1 group Opening library file /home/tianwd/soft/gromacs4//share/gromacs/top/aminoacids.dat Group 0 ( System) has 5204 elements Group 1 ( SOL) has 5168 elements Group 2 ( CL-) has18 elements Group 3 ( NA+) has18 elements Select a group: 0 Selected 0: 'System' Reading frame 0 time 1000.000 --- Program g_rdf, VERSION 4.0.4 Source code file: gmx_rdf.c, line: 639 Fatal error: Error: atom (MW) not in list (5 types checked)! --- Thanks in advance -- wende ___ 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] 43A1-S3 FF
Dear gmx developer, I have read the paper* An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers J. Phys. Chem. B 2748 2009, 113, 2748–2763* Is the new force field (43A1-S3) can instead of the FF of Berger et al. for lipid simulations? When will it be incorporated in the Gromacs package? Thanks in advance. -- wende ___ 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] about epsion_surface
I want to know the arithmetic of GROMACS for dealing with epsion_surface. Any ref. paper? Because I donot know Why the manual give a note about this parameter: Be careful - you shouldn’t use this if you have free mobile charges in your system. Thanks in advance. -- wende ___ 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] epsion_surface
Hi, I do not know why the manual give a note about the parameter of epsion_surface : Be careful - you shouldn’t use this if you have free mobile charges in your system. WHY? Could some kind people give me an explanation or some references? Thanks in advance. ___ 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] fatal error when using Martini CG force field
When I use CG martini force field to do simulation, and use the example of Martini website. There are many warnings when grompp the mdp file: -- WARNING 4 [file mem16.top, line 41]: For proper thermostat integration tau_t (0.1) should be more than an order of magnitude larger than delta_t (0.02) - After running long time, a fatal error appears: Fatal error: 1 of the 13956 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck What does it matter? Thanks in advance -- wende ___ 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] Re: fatal error when using Martini CG force field
I use the gmx4.04 version. The detail error information is as follows. May be there is a bug in domain decompostion method because someone met this problem beforce. Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 3704 missing 1 Molecule type 'DEN' the first 10 missing interactions, except for exclusions: G96Angle atoms 62 129 130 global 5162 5229 5230 --- Program mdrun_mpi, VERSION 4.0.4 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 13956 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck -- wende ___ 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] Problem in Martini simulation with gromacs version 4.0.4 works fine with gromacs 3.3.1 error G96Angle of 2395 missing
I meet the same problem. Have you delt with it? What's the Matter? Thanks in advance. -- wende ___ 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] zero surface tension
Hello everyone, In the literature, Many reports use the lateral and normal pressures independently coupled to a pressure of 1 bar for bio-membrane simulations. I want to know whether it can guarantee the zero surface tension of the membrane. If not, which situation it can not guarantee. Any suggestion is appreciated. Thanks in advance. -- wende ___ 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] about epsion_surface
Dear, I do not know where should I have to use the epsion_surface? The system include a CG membrane, a charged macromolecule above the membrane and some counterions ? It is suitable to using this parameter epsilon_surface = 1? It is appricated if some one tell me something about how to use this parameter. Thanks in advance. -- wende ___ 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] say something about the pull geometry of cylinder
Hi , I can not fully understand the picture of parameter of pull geometry of cylinder. Who can say something about it, Thanks in advance. Thanks in advance. - pull geometry cylinder Designed for pulling with respect to a layer where the reference COM is given by a local cylindrical part of the reference group. The pulling is in the direction of pull vec,which should have only a z-component. From the reference group a cylinder is selected for determining the COM, with the axis given by the x/y location of the group to be pulled and two radii. The radius pull r1 gives the radius within which all the relative weights are one, between pull r1 and pull r0 the weights are switched to zero. Mass weighting is also used. -- wende ___ 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] How to understand the pull geometry of cylinder
Hi everyone, My colleague and I can not understand the picture of parameter of pull geometry of cylinder. How to determine the reference COM? How does the pulled group move? It is apprecited if someone gives me a simple picture of the parameter. A sketch map is OK. Thanks in advance. - pull geometry cylinder Designed for pulling with respect to a layer where the reference COM is given by a local cylindrical part of the reference group. The pulling is in the direction of pull vec,which should have only a z-component. From the reference group a cylinder is selected for determining the COM, with the axis given by the x/y location of the group to be pulled and two radii. The radius pull r1 gives the radius within which all the relative weights are one, between pull r1 and pull r0 the weights are switched to zero. Mass weighting is also used. -- wende ___ 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] about martini forcefield(MFF)
Dear , I do MD simulation with Martini Force Field. There are about 2048 DPPCs in my system. But I don't know how many.water molecules should be added to system of (25 25 17)nm . Is it important that the ratio of water/DPPC for DPPC behavior? Can I add water arbitrarily, such as 7 or more? I read many papers, It seems that the ratio is not fixed in different system. So, It is appreciated if some kind people give me some advice about how to choose water/dppc. Thanks in advance -- wende ___ 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] about MARTINI forcefield
Hi MARTINI forcefield users, I am very interesting in using the MARTINI forcefield for simulating my molecules, But I am not very familiar with it. So I hope some kind people can help me about its application. I want to know if It is suitable for the molecules of attached figures. It have TWO joint benzenes and ONE linked benzenes. If it is, what I should take care of ? Thanks in advance. -- Wende Tian Email:wende1...@gmail.com Tel:025-83595329 Address: National Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210093, China === attachment: mo.jpg___ 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] How to carry out rigid body
Hi everyone, I want to peform CG-MDs with gromacs. In my system, there are some rigid bodies which are composed by hundreds of LJ atoms. Atoms of each rigid body move together in LJ water solution. How can I deal with it? Any suggestion is appreciated. Thanks in advance. -- wende ___ 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
