Re: [gmx-users] velacc & box of water
Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? Can't comment on the first part...maybe the code will point you in the right direction? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot This task might be approached in a couple of ways: 1. genconf -nbox to define a suitable number of replicate systems. 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only the desired number of molecules. -Justin to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] velacc & box of water
Jamie Seyed wrote: Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie genconf will allow you to stack multiples of that 216 box. Or, use editconf to adjust the size of a 216 box, and genbox to fill it to get a number that suits your fancy. In either case you will need to equilibrate before trying to measure velacc, just as with any other observable. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] velacc & box of water
Dear Gmx Users, I have a 2 questions. First about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another recent post that said it has been included in the code... Would you please clarify this that if I need the factors or not. Also I found 2 numbers after integration. Integral 1 0.01595 setaverage SS1 3.718082e-04 --1) Would you please inform me what are these number and what is the relation between them? --2) My second question is I want to make a box of only water (spce) with let say 500 water molecules. Would you please give me quick hints how to do it (the proper way) or refer me to good point? Up to now I can only have 216 water molecules from tuto/water folder and I tried a lot to start from the beginning, but I could not make it... I appreciate if you help me to understand the first issue and be able to overcome the second one. Many Thanks in Advance/Jamie ___ 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] Question about genion, error happens
Hi Pan Wu, You use -pname to specify that the added sodium ions should have the name 'Na'. Accordingly, at the end of your .top file genion writes a line under [ System ] specifying the number of 'Na' molecules. But that requires that 'Na' is defined, which is not the case, given the error. The correct name for sodium that you have to use depends on the force field you use. In ions.itp there are definitions for different force fields, but each may use its own name. Maybe you should've used 'NA' or 'NA+'? Cheers, Tsjerk On Sat, Oct 10, 2009 at 5:06 PM, Pan Wu wrote: > Hi gmx users, > My system has two protein chain + solvent, and the total charge is -12. > I use "genion" to add 12 Na+ in the *.tpr and *.top file. > However there is some fatal error happens when I try to regenerate the > new tpr file for calculation, it really confuse me. > The process and error msg is below: > 1. genion_d -s neg_charge.tpr -nice 0 -np 12 -pname Na -rmin 0.6 -p > system_neg.top -o out.gro -g genion.log > Then the topology file is updated, with some Na added. change name into > system_neu.top > 2. copy ions.itp in the current folder, add #include "ions.itp" in > system_neu.top > > 3. Then I use > grompp -f for_md.mdp -c out.gro -p system_neu.top -o md_run.tpr > -maxwarn 1000 >& gen_tpr.log > try to get the new md_run.tpr. > The error message is: "No such moleculetype Na" > I don't know how to revise the ions.itp file, and did not revise that. > Thank you in advance! > > > > -- > Sincerely > = > Pan Wu > Graduate Student in Department of Chemistry > Duke University > 124 Science Drive > 5301 French Family Science Center > Durham, NC 27708 > Phone: (919) 660-1583 > = > > > ___ > gmx-users mailing list gmx-us...@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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 genion, error happens
Hi gmx users,My system has two protein chain + solvent, and the total charge is -12. I use "genion" to add 12 Na+ in the *.tpr and *.top file. However there is some fatal error happens when I try to regenerate the new tpr file for calculation, it really confuse me. The process and error msg is below: 1. genion_d -s neg_charge.tpr -nice 0 -np 12 -pname Na -rmin 0.6 -p system_neg.top -o out.gro -g genion.log Then the topology file is updated, with some Na added. change name into system_neu.top 2. copy ions.itp in the current folder, add #include "ions.itp" in system_neu.top 3. Then I use grompp -f for_md.mdp -c out.gro -p system_neu.top -o md_run.tpr -maxwarn 1000 >& gen_tpr.log try to get the new md_run.tpr. The error message is: "No such moleculetype Na" I don't know how to revise the ions.itp file, and did not revise that. Thank you in advance! -- Sincerely = Pan Wu Graduate Student in Department of Chemistry Duke University 124 Science Drive 5301 French Family Science Center Durham, NC 27708 Phone: (919) 660-1583 = ___ 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] how to calculate the non-bond interaction between solvent and solvent in pure solvent system
I want to calculate the non-bond interaction (LJ+Coulomb) between solvent and solvent in pure solvent system. After the simulation of my pure solvent system, I calculated the interaction between solvent and solvent using the rerun option of the "mdrun program". First, I set the energygrps = sol sol in rerun.mdp file. Then, I make the grompp program like this, grompp -f rerun.mdp -c conf.gro -n index.ndx -p pure.top -o rerun.tpr But this step has a fatal error: Atom 1 in multiple energy Mon. groups (1 and 2) This option can only calculate energies between non-overlapping groups. That what he message is telling you: one atom can not be part of more than one group. If you actually have a simulation of pure solvent the total non-bonded energy of your system seems to be what you are looking for! I don't know how to solve the problem and I want to know whether this method is effective for calculating the interaction between solvent and solvent in pure solvent system. Any suggestion will be appreciated. Jinyao Wang wan...@ciac.jl.cn 2009-10-10 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to calculate the non-bond interaction between solvent and solvent in pure solvent system
Jinyao Wang wrote: Hi gmx-users， I want to calculate the non-bond interaction (LJ+Coulomb) between solvent and solvent in pure solvent system. After the simulation of my pure solvent system, I calculated the interaction between solvent and solvent using the rerun option of the "mdrun program". First, I set the energygrps = sol sol in rerun.mdp file. Then, I make the grompp program like this, grompp -f rerun.mdp -c conf.gro -n index.ndx -p pure.top -o rerun.tpr But this step has a fatal error: Atom 1 in multiple energy Mon. groups (1 and 2) I don't know how to solve the problem and I want to know whether this method is effective for calculating the interaction between solvent and solvent in pure solvent system. Any suggestion will be appreciated. These terms should already be present in the .edr file. Run g_energy and have a look. -Justin Jinyao Wang wan...@ciac.jl.cn 2009-10-10 ___ 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to calculate the non-bond interaction between solvent and solvent in pure solvent system
Hi gmx-users， I want to calculate the non-bond interaction (LJ+Coulomb) between solvent and solvent in pure solvent system. After the simulation of my pure solvent system, I calculated the interaction between solvent and solvent using the rerun option of the "mdrun program". First, I set the energygrps = sol sol in rerun.mdp file. Then, I make the grompp program like this, grompp -f rerun.mdp -c conf.gro -n index.ndx -p pure.top -o rerun.tpr But this step has a fatal error: Atom 1 in multiple energy Mon. groups (1 and 2) I don't know how to solve the problem and I want to know whether this method is effective for calculating the interaction between solvent and solvent in pure solvent system. Any suggestion will be appreciated. Jinyao Wang wan...@ciac.jl.cn 2009-10-10 ___ 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
