[gmx-users] Question about ffamber in Gromacs
Dear gromacs user, I am doing the MD simulation of CNT-DNA interaction. Before introducing DNA, I used gromacs default force field and finished the simulation of CNT (carbon nanotube). And, in the ffgmxnb.itp, I introduced the non-bonded parameters for C-C and C-OW (oxygen) in the [non-bonded param] session. Now, I have the amber99 package. I opened ffamber99nb.itp and compared the format of ffamber99nb.itp to ffgmxnb.itp. There is only [atoms] session in ffamber99nb.itp. Do you mind telling me how to introduce these non-bonded parameters (L-J parameters) for C-C and C-OW in ffamber? Do I just simply add [non-bonded param] at the end of the ffamber99nb.itp and list the parameters there? I guess this is important for me because I attempted to add [non-bonded param] at the end of the itp file. After the energy minimization, I visualized that the carbon nanotube is standing above the simulation box. Also, I realize that the atom mass in ffamberXX.itp is 0, but in ffamberXX.atp, all masses are non-zero. Do you minding explain it for me in detail? I appreciate your help. Regards! Bo ___ 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] Question about CNT simulation
Dear gromacs user, I am doing a CNT-water simulation with using ffamber99 forcefield. I don't know what carbon and hydron atom models I should use. In ffamber99.atp, there are a lot of different C atoms with same mass. Can you give me some suggestion? Cheers! Bo ___ 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] about CNT simulation
Dear gromacs users, Thank you for your answering my previous questions. Here, I am in trouble again. I continue the simulation of DNA, carbon nanatube and water. I changed the names of atoms in cnt.pdb according to the names in ffamberXX.itp. When I performed the energy minimization, the result I get is : "Fatal error: Invalid order for directive defaults, file ""ffamber99.itp"", line 4". I checked back ffamber99.itp, the whole file is simple : "#define _FF_AMBER #define _FF_AMBER99 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 #include "ffamber99nb.itp" #include "ffamber99bon.itp" " Can you give me some suggestions and help me out? Also, I have a question regarding the residue names in amber99. I guess that I may also need to change the residue of CNT(carbon nanotube) according to the residue names used in ffamber99. Do you think that it is necessary? And, how can I do it? Thank you so much! Bo ___ 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] Question about MD simulation
Dear gromacs users, I have a quetion regarding using amber forcefield in gromacs. I did the DNA and water interaction simulation. After the energy minimization, the original helix-structured DNA becomes two fragments. At this stage, I assume that the "simulation process" is correct. I used exactly same energy minimization em.mdp file for my nanotube-water simulation. Since I am using amber forcefield, I changed the name of all atoms (C, H) of my nanotube according to the name used in ffamberXX.itp. For example, C is renamed as amberXX_42. During the energy minimization, I got warning messages as: WARNING: Writing out atom name (amber) longer than 4 characters to .pdb file Also, the EM result is "Segmentation Fault". Can anyone give me some suggstions or hints how to solve the problem? Is there any other ways to rename those atoms (either in NT or amber files)? Thank you very much! Bo ___ 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] Question about DNA simulation
Hello, I have a question regarding DNA simulation. I have the amber99 package. Can anyone give me an explanation why all the masses in the ffamberXXnb.itpare 0? Thank you very much! Bo ___ 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] Question about DNA simulation
Hi, As I mentioned in my last message, I also use pymol to visualize the molecule with water. I realize that the very top part of the DNA molecule is not surrounded by water molecules. I tried to varying the value for -d. Do you have any suggestions? Cheers~ Bo ___ 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] Question about DNA simulation
Hi everyone, I am still lost. For the DNA simulation that I am doing, I really don't know what is wrong. Is the em.mdp file (maybe temperature or other settings) inappropriate? Can you give me more specified explanation? Regards! Bo ___ 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] Question about DNA simulation
Hi, When I do the DNA MD simulation. I use pdb2gmx, and the water model I used is spc.gro. I did the editconf and genbox. The following is my em.mdp file. define =-DEFLEXIBLE integrator = steep ;gen-vel = yes ;pbc = no ;comm_mode = angular nsteps = 2000 epsilon_rf = 82 nstlist = 100 ns_type = grid rlist = 1.3 dt = 0.0005 tc-grps = system tcoupl = Berendsen ;freezegrps = CNT ;freezedim = N tau-t = 0.1 temp= 450 ref-t = 450 ;pcoupl = Parrinello-Rahman ;pcoupltype = isotropic ;tau-p = 0.5 ;ref_p = 1.01325 ;compressibility = 4.5e-5 coulombtype = pme rcoulomb= 1.3 vdw-type= cut-off rvdw= 1.3 nstenergy = 10 optimize_fft= yes emstep = 0.2 emtol = 100 constraints = none - Q1, I am not sure whether should I put the "define = -DFLEXIBLE" in the em.mdp. Q2, When I perform the preprocess for energy minimization (grompp), the error message is : "Fatal error: [file "/home/nano/gromacs/share/gromacs/top/spc.itp", line 41]: Atom index(1) in setttles out of bounds (1-0)" I looked back to the spc.itp, from line 39 to 41: -- [ settles ] ; OWfunctdohdhh 110.10.16330 - Can you give me any suggestions about how to correct it and why? Best regards! Bo ___ 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] Problems with forcefield amber99 in Gromacs
Hi, I have a question regarding to using forcefield amber99 in Gromacs. I have all the parameter files of amber99. I am doing the MD of carbon nanotube with DNA. I have changed the .pdb file of the DNA according to the instruction. I generated the topology of DNA with identifying -water tip5p.gro. The topology file of DNA is also generated successful. Pymol is used to visualize the DNA structure. Now, I am doing the energy minimization. When I use the grompp command, the output is that "Fatal error: No such moleculetype SOL". I am wondering can anybody tell me how to use the tip5p model of water. Also, actually, I want to do the simulation with tip3p. But I could not find tip3p.gro. I checked back. There was also another person asked the same question. But, I don't quite following the answer. Do you minding telling me more about the process? ___ 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
