Re: [gmx-users] Potential Energy
I did not develop the force field of my molecule by myself. In stead I use the literature force field parameters. I guess not all the force field need the [pairs]. As long as I can get reasonable experimental observables, I can use such force field, right? On Tue, Jan 26, 2010 at 6:50 PM, Mark Abraham wrote: > > > - Original Message - > From: Yanmei Song > Date: Wednesday, January 27, 2010 10:58 > Subject: Re: [gmx-users] Potential Energy > To: jalem...@vt.edu, Discussion list for GROMACS users < > gmx-users@gromacs.org> > > > Dear Justin: > > > > I finally figure out that the problem comes from the Coulomb 1-4 > interactions defined by [pairs] part. When I remove this parts, the energy > minimization ends with a big negative number. Thanks for your help. > > That's not a solution, that's a random number generator. Whether or not you > need such pairs is force-field dependent. Ad hoc changes are ridiculous. > Messing with force fields is an expert topic, and parameterizing a new > molecule is difficult and risky. > > 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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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] Potential Energy
Dear Justin: I finally figure out that the problem comes from the Coulomb 1-4 interactions defined by [pairs] part. When I remove this parts, the energy minimization ends with a big negative number. Thanks for your help. On Tue, Jan 26, 2010 at 4:24 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Sorry, that itp is the original one generated by PRODRG. Also I have >> modified it based on a optimized force field of the molecule. (See attached >> file and the literature of the force field). But still the potential energy >> is positively 1e2 and why the system can run well and I can get the >> reasonable density? Except charge, can you see any obvious mistakes of the >> itp file? since even if the parameter is not so optimized, I should not get >> such a big positive potential energy. >> >> > If you have 27800 molecules, that means you have almost 56000 -OH groups > and even more potential H-bond acceptors with the ether oxygens. If there > are a lot of unoccupied hydrogen bonding groups, then you have a lot of > electrostatic interactions that are unsatisfied. The same situation can > occur with, for example, a protein in vacuum. I'm assuming this is the > case, but you haven't said whether or not there's solvent. > > As for whether or not you can lump the hydrogen charges into the carbon > atoms, that can be debated. The parameter set you've used has no direct > relevance to the Gromos parameter set from which you're (presumably) taking > atom types. But if you're able to produce a substantial amount of > experimental observables, you may be able to justify your methods. > > -Justin > > > -- > > > 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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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] Potential Energy
Dear Users: I am in the process of setting up a new system. I have a 8.0*8.0*8.0 nm3 system which include 27800 molecules. When the system approach equilibrium, I found the potential energy is +3e5 (big positive number). Is this normal? Since based on my experience, for systems in such size, the potential energy is usually a big negative number? Does this mean that my force field parameter or molecule structure have problems? Thanks in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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] OPLS force field
Dear Users: I build up my polymer molecules in PRODRG and got the .gro and .itp file. Then anyone knows how I can transfer or edit the itp file into OPLS force field format? Or anyone knows how can I get the OPLS force field parameters if I have my molecule gro file. Any suggestion will be great thankful. -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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] Why density increase with increasing the cutoff length?
Thanks for all the helpful response. But do I have to use dispersion correction when I use PME? I don't quite understand what dispersion correction do. Sometime I found using dispersion correction make my results worse for a large molecule system. On Mon, Dec 21, 2009 at 12:48 AM, David van der Spoel wrote: > On 12/21/09 8:03 AM, Yanmei Song wrote: > >> Dear Users: >> >> Anyone can explain why the density of the water models increase with >> increase the cutoff length. I tried a couple water models in >> reaction-field, PME simulations.The cutoff length ranged from 0.9 to >> 1.5. They all show the same trend. Then there must be some reasons. >> Anyone can tell me why? >> >> -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> Van der Waals interactions. I guess you have not turned on the dispersion > correction. If you do the effect should be far less. > > -- > 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 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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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] Why density increase with increasing the cutoff length?
Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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 block averaging error from non-equilibrium MD simulations
Dear Justin: Thank you so much for your quick response. But I still don't get it. Should I calculate the standard error manually by using the equations A17 (in B. Hess' s paper) after I get the result by g_analyze. And then which value I should use for the sigma? Here is the output : invalid fit: e.e. 15.6513 a 2.17585 tau1 28.9321 tau2 46.3966 Will use a single exponential fit for set 1 Set 1: err.est. 21.0339 a 1 tau1 15.1648 tau2 0 I really appreciate your patience and help! On Fri, Nov 20, 2009 at 3:07 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> I really appreciate your response and help! >> >> I am confusing about the result by using this method. I found in B. Hess's >> paper (Appendix, JCP, 116, 2002) that " this gives a standard error >> estimate for 1/eta of 29.5. "; and the error he gives for that eta is 0.006. >> I thought the error should be calculated as 1/29.5=0.034. Thank you again >> for your help! >> >> > The relationship is not a simple inversion as you've shown it. That is, > (standard error of 1/eta) != 1/(standard error of eta). The standard error > calculation depends on a number of factors, hence all the math in the > Appendix :) An example is given in Fig. 8 of that paper. > > -Justin > > > -- > > > 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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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 block averaging error from non-equilibrium MD simulations
Dear Justin: I really appreciate your response and help! I am confusing about the result by using this method. I found in B. Hess's paper (Appendix, JCP, 116, 2002) that " this gives a standard error estimate for 1/eta of 29.5. "; and the error he gives for that eta is 0.006. I thought the error should be calculated as 1/29.5=0.034. Thank you again for your help! On Fri, Nov 20, 2009 at 12:35 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Users: >> >> Anyone knows how to get the standard errors of the results based on block >> averaging from non-equilibrium MD simulations? I am trying to get the error >> estimations for my calculated viscosity of the fluid. Any command can give >> me that? or I have to do it manually? Thank you in advance! >> > > From g_analyze -h: > > "Option -ee produces error estimates using block averaging. A set is > divided > in a number of blocks and averages are calculated for each block. The error > for the total average is calculated from the variance between averages of > the > m blocks B_i as follows..." > > -Justin > > > >> -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> > -- > > > 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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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 block averaging error from non-equilibrium MD simulations
Dear Users: Anyone knows how to get the standard errors of the results based on block averaging from non-equilibrium MD simulations? I am trying to get the error estimations for my calculated viscosity of the fluid. Any command can give me that? or I have to do it manually? Thank you in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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] bonds that rotated more than 30 degrees:
Dear Users: I used all-bonds for constraints. My MD is dead right after i submit the task. The error message is : Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2.084475 (between atoms 23417 and 23431) rms 0.054595 bonds that rotated more than 30 degrees: Anyone knows what is the problem and how i can fix it? Thanks -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] MD fatal error :wrong string length 0 for string buf
what version is the tpr file? The one corresponding to mdrun 3.3.3? What do you mean? I used gromacs-3.3.3 before and now. the same system and I did not have the problem before. On Thu, Oct 29, 2009 at 2:06 PM, David van der Spoel wrote: > Yanmei Song wrote: > >> Dear All: >> >> When I submitted the md run, It gives me the following error: >> >> Program mdrun, VERSION 3.3.3 >> Source code file: gmxfio.c, line: 607 >> >> Fatal error: >> wrong string length 0 for string buf (source tpxio.c, line 1150) >> >> I run the similar system before using the same md.mdp file. and it was >> fine. >> >> what version is the tpr file? The one corresponding to mdrun 3.3.3? > >> Any suggestions would be greatly appreciated >> Thanks >> >> >> -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> >> ___ >> 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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] MD fatal error :wrong string length 0 for string buf
Dear All: When I submitted the md run, It gives me the following error: Program mdrun, VERSION 3.3.3 Source code file: gmxfio.c, line: 607 Fatal error: wrong string length 0 for string buf (source tpxio.c, line 1150) I run the similar system before using the same md.mdp file. and it was fine. Any suggestions would be greatly appreciated Thanks -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 get the rotational correlation time of the non-equilibrium simulation
Dear Users: I am wondering how I can get rotation correlation time of non-equilibrium simulation? is there any command letting me do that? Or I have to do it manually? My second question is : if Gromacs can calculate the standard error by using the blocking average method and how? Thanks for your help in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] The Cut-off for coulombtype heat up the water system?
Dear Justin: Thank you so much for your answer. That helps a lot! On Thu, Jun 18, 2009 at 10:35 AM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Thanks for your response. >> >> The reason I am doing this is that I wanted to test what the different >> electrostatics treatments will affect my results. So the heating up is >> normal by using a plain cut-off and the results can not be trusted, right? >> >> > That is one of the known problems with using cut-off, yes. > > -Justin > > On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Yanmei Song wrote: >> >>Dear Users: >> >>I was running a system by non-equilibrium MD using a plain >>Cut-off for the electrostatics: >> >>title = water >>cpp = /lib/cpp >>constraints = all_bonds >>integrator = md >>dt = 0.004 ; ps ! >>nsteps = 50 ; total 8ns. >>nstcomm = 1 >>nstxout = 5 >>nstvout = 5 >>nstfout = 0 >>nstlog = 5000 >>nstenergy = 5000 >>nstxtcout = 25000 >>nstlist = 10 >>ns_type = grid >>pbc = xyz >>coulombtype = Cut-off >>rlist = 0.8 >>rcoulomb= 0.9 >>rvdw= 0.8 >>fourierspacing = 0.12 >>ewald_rtol = 1e-5 >>;nemd >>cos_acceleration= 0.005 >>; Berendsen temperature coupling is on in two groups >>Tcoupl = berendsen >>tc_grps = SOL >>tau_t = 0.1 >>ref_t = 300 >>; Energy monitoring >>energygrps = SOL >>; Isotropic pressure coupling is now on >>Pcoupl = berendsen >>pcoupltype = isotropic >>;pc-grps= SOL >>tau_p = 1.0 >>ref_p = 1.0 >>compressibility = 4.5e-5 >> >>; Generate velocites is off at 300 K. >>gen_vel = yes >>gen_temp= 300.0 >>gen_seed= 10 >> >> I can not figure out where I did wrong, the temperature of the >>system is 303.54 after 5ns run ( the temperature turns to 303 in >>500ps). Thanks for the help in advance! >> >> >>Why are you using cutoff for coulombtype? It is the reason for the >>heating you are seeing: >> >> >> http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html >> >>-Justin >> >>--Yanmei Song >>Ph.D. Candidate >>Department of Chemical Engineering >>Arizona State University >> >> >> >> >> >>___ >>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/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/mailing_lists/users.php >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>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@gromacs.org >><mailto:gmx-users@gromacs.org> >>http://lists.gromacs.org/mailman
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Users: >> >> I was running a system by non-equilibrium MD using a plain Cut-off for the >> electrostatics: >> >> title = water >> cpp = /lib/cpp >> constraints = all_bonds >> integrator = md >> dt = 0.004 ; ps ! >> nsteps = 50 ; total 8ns. >> nstcomm = 1 >> nstxout = 5 >> nstvout = 5 >> nstfout = 0 >> nstlog = 5000 >> nstenergy = 5000 >> nstxtcout = 25000 >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> coulombtype = Cut-off >> rlist = 0.8 >> rcoulomb= 0.9 >> rvdw= 0.8 >> fourierspacing = 0.12 >> ewald_rtol = 1e-5 >> ;nemd >> cos_acceleration= 0.005 >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = berendsen >> tc_grps = SOL >> tau_t = 0.1 >> ref_t = 300 >> ; Energy monitoring >> energygrps = SOL >> ; Isotropic pressure coupling is now on >> Pcoupl = berendsen >> pcoupltype = isotropic >> ;pc-grps= SOL >> tau_p = 1.0 >> ref_p = 1.0 >> compressibility = 4.5e-5 >> >> ; Generate velocites is off at 300 K. >> gen_vel = yes >> gen_temp= 300.0 >> gen_seed= 10 >> >> I can not figure out where I did wrong, the temperature of the system is >> 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for >> the help in advance! >> > > Why are you using cutoff for coulombtype? It is the reason for the heating > you are seeing: > > http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html > > -Justin > > -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> >> >> >> ___ >> 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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] The Cut-off for coulombtype heat up the water system?
Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] Viscosity using periodic perturbation method
Dear Berk: Thank you so much for your help! I read your paper: " Determing the shear viscosity of model liquids from molecular dynamics simulations" You used NVT? My question is which one is better? NPT or NVT? "Strictly speaking it might be incorrect, but since pressure scaling is usually less than 1% it will not affect your results significantly." So technically we should use NVT for the periodic perturbation method, right? Thanks! On Tue, May 26, 2009 at 12:03 AM, Berk Hess wrote: > Hi, > > Yes, you can use NPT, the code takes care of this properly. > Strictly speaking it might be incorrect, but since pressure scaling is > usually less than 1% > it will not affect your results significantly. > > Berk. > > -- > Date: Mon, 25 May 2009 15:19:10 -0700 > From: yson...@asu.edu > To: gmx-users@gromacs.org > Subject: [gmx-users] Viscosity using periodic perturbation method > > > Dear users: > > I was trying to calculate the viscosity of liquid system using periodic > perturbation method. Does this method require NVT ensemble simulation in > stead of NPT ? Because I read some literature on periodic perturbation > method. they all used NVT. I did not found any information about this on > the manual. Can I use NPT Non-equilibrium MD in order to use periodic > perturbation method? Thanks in advance! > -- > Yanmei Song > Ph.D. Candidate > Department of Chemical Engineering > Arizona State University > > -- > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > ___ > 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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] Viscosity using periodic perturbation method
Dear Herk: Thank you so much for your help! Maybe the way I asked make it confusing. I read your paper: " Determing the shear viscosity of model liquids from molecular dynamics simulations" You used NVT. My question is which one is better? NPT or NVT? Or you can use either of them. "Strictly speaking it might be incorrect, but since pressure scaling is usually less than 1% it will not affect your results significantly." So technically we should use NVT for the periodic perturbation method, right? Thanks! On Tue, May 26, 2009 at 12:03 AM, Berk Hess wrote: > Hi, > > Yes, you can use NPT, the code takes care of this properly. > Strictly speaking it might be incorrect, but since pressure scaling is > usually less than 1% > it will not affect your results significantly. > > Berk. > > -- > Date: Mon, 25 May 2009 15:19:10 -0700 > From: yson...@asu.edu > To: gmx-users@gromacs.org > Subject: [gmx-users] Viscosity using periodic perturbation method > > > Dear users: > > I was trying to calculate the viscosity of liquid system using periodic > perturbation method. Does this method require NVT ensemble simulation in > stead of NPT ? Because I read some literature on periodic perturbation > method. they all used NVT. I did not found any information about this on > the manual. Can I use NPT Non-equilibrium MD in order to use periodic > perturbation method? Thanks in advance! > -- > Yanmei Song > Ph.D. Candidate > Department of Chemical Engineering > Arizona State University > > -- > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > ___ > 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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] Viscosity using periodic perturbation method
Dear users: I was trying to calculate the viscosity of liquid system using periodic perturbation method. Does this method require NVT ensemble simulation in stead of NPT ? Because I read some literature on periodic perturbation method. they all used NVT. I did not found any information about this on the manual. Can I use NPT Non-equilibrium MD in order to use periodic perturbation method? Thanks in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] shift function for vdwtype and density
Dear all: This is the mdp I just used for the system. The funny thing is after a 8ns simulation I got a very high pressure and temperature: Temperature 343.437 Pressure (bar) 45.782 I also did another run with removing the vdw_switch in mdp and keep all other condition unchanged. I got good result. The following is my mdp: cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 2000 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = Shift rvdw_switch = 0.8 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.0 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = PDM ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 On Tue, May 19, 2009 at 11:12 AM, Yanmei Song wrote: > Dear David: > > Thank you so much for the valuable information. > > "Our conclusion in the above paper is to use PME for Coulomb and not shift > Van der Waals" > > I have read the paper you mentioned and did not find how you treated the > VdW. Have you done some work on the cut off method for vdw? Since I used PME > for Coulomb in my system. I am still confusing why not shift for vdw. > > " I would also recommend to use TIP4P rather than TIP5P, as Jorgensen uses > TIP4P for all his parameterizations." > > I have read Jorgensen's paper for the OPLS and realized that the TIP4P > would be the first choice for combining with OPLS. However my concern is > that TIP4P model is not as good as TIP5P in terms of diffusion constant and > viscosity which are extremely important for my purpose. > > I also have compared SPC and TIP4P and turn out that SPC can give a better > result for my system. Unfornately SPC has a very bad viscosity as TIP4P. So > I am trying TIP5P. > > Do you think OPLS+ TIP5P can cause serious problem or horrible artifacts. > If you can suggest some literatures on this that would be great. > > I really appericate all your help! > > On Mon, May 18, 2009 at 10:37 PM, David van der Spoel < > sp...@xray.bmc.uu.se> wrote: > >> Justin A. Lemkul wrote: >> >>> >>> >>> Yanmei Song wrote: >>> >>>> Dear Justin: >>>> >>>> Yes and I tried dispersion correction and it gives a larger density than >>>> I expected. The density of the polymer by vdwtype=shift is more close to >>>> the experimental value. Then your suggestion would be to choose the >>>> vdwtype=cut-off under this condition even if it result in larger density? >>>> Thank you so much! >>>> >>>> >>> No. My suggestion is to do your homework, as Mark originally said, and >>> as I echoed in my last mail. Read about the water model, its expected >>> performance under different simulation parameters, and evaluate what you >>> want to do once you have done this background work. If you have done a >>> thorough literature review, there is no one else that can make a choice for >>> you; decide how to handle your system based on what you read. >>> >>> Actually this is not so easy. Jorgensen has never published the way he >> treats cut-offs, but he was friendly enough to let me know, so we have >> actually done it: >> David van der Spoel and Paul J. van Maaren: The origin of layer structure >> artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11 >> (2006) >> >> If you look in the appendix you can find the "one and only" > > > >> OPLS. However This is not to be recommended since the effect is very >> different for MD and MC (what Jorgensen uses). In MD the official method >> will give horrible artifacts. In other words, you have to use something >> better. Our conclusion in the above paper is to use PME for Coulomb and not >> shift Van der Waals. I would also recommend to use TIP4P rather than TIP5P, >> as Jorgensen uses TIP4P for all his parameterizations. >> >> >> >> >> -Justin >>> >>&
Re: [gmx-users] shift function for vdwtype and density
Dear David: Thank you so much for the valuable information. "Our conclusion in the above paper is to use PME for Coulomb and not shift Van der Waals" I have read the paper you mentioned and did not find how you treated the VdW. Have you done some work on the cut off method for vdw? Since I used PME for Coulomb in my system. I am still confusing why not shift for vdw. " I would also recommend to use TIP4P rather than TIP5P, as Jorgensen uses TIP4P for all his parameterizations." I have read Jorgensen's paper for the OPLS and realized that the TIP4P would be the first choice for combining with OPLS. However my concern is that TIP4P model is not as good as TIP5P in terms of diffusion constant and viscosity which are extremely important for my purpose. I also have compared SPC and TIP4P and turn out that SPC can give a better result for my system. Unfornately SPC has a very bad viscosity as TIP4P. So I am trying TIP5P. Do you think OPLS+ TIP5P can cause serious problem or horrible artifacts. If you can suggest some literatures on this that would be great. I really appericate all your help! On Mon, May 18, 2009 at 10:37 PM, David van der Spoel wrote: > Justin A. Lemkul wrote: > >> >> >> Yanmei Song wrote: >> >>> Dear Justin: >>> >>> Yes and I tried dispersion correction and it gives a larger density than >>> I expected. The density of the polymer by vdwtype=shift is more close to >>> the experimental value. Then your suggestion would be to choose the >>> vdwtype=cut-off under this condition even if it result in larger density? >>> Thank you so much! >>> >>> >> No. My suggestion is to do your homework, as Mark originally said, and as >> I echoed in my last mail. Read about the water model, its expected >> performance under different simulation parameters, and evaluate what you >> want to do once you have done this background work. If you have done a >> thorough literature review, there is no one else that can make a choice for >> you; decide how to handle your system based on what you read. >> >> Actually this is not so easy. Jorgensen has never published the way he > treats cut-offs, but he was friendly enough to let me know, so we have > actually done it: > David van der Spoel and Paul J. van Maaren: The origin of layer structure > artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11 > (2006) > > If you look in the appendix you can find the "one and only" > OPLS. However This is not to be recommended since the effect is very > different for MD and MC (what Jorgensen uses). In MD the official method > will give horrible artifacts. In other words, you have to use something > better. Our conclusion in the above paper is to use PME for Coulomb and not > shift Van der Waals. I would also recommend to use TIP4P rather than TIP5P, > as Jorgensen uses TIP4P for all his parameterizations. > > > > > -Justin >> >> On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote: >>> >>> >>> >>>Yanmei Song wrote: >>> >>>Dear Justin: >>> >>>Yes. Before I do the water+polymer, I did both the bulk systems >>>separately. The density of TIP5P I mentioned earlier is the >>>results for pure water bulk system. My concern is that if it is >>>reasonable that the property of the system changes with >>>different mdp conditions? Since when I did the bulk water and >>>bulk polymer system, I found the densities change with different >>>cutoff and vdwtype conditions. Is this a artifact? Or the larger >>>cutoff, the more accurate result we can get? >>> >>> >>>Every parameter you specify will affect the results you see. I >>>agree with Mark - look up the original reference for TIP5P and see >>>what parameters are recommended. Also read the subsequent >>>literature that has used TIP5P to see what modifications >>>(electrostatic treatment, vdW treatment, etc) are appropriate or >>>even more accurate. >>> >>>Also realize that using vdwtype = shift may not be the best >>>solution. I only suggested as a guess for something to try back >>>when you were getting bizarre results with your polymer. Have you >>>ever tried dispersion correction when using vdwtype = cutoff? I >>>routinely use such a setup and have never seen any really bizarre >>>behavior. >>> >>>-Justin >>> >>>On Mon
Re: [gmx-users] shift function for vdwtype and density
Dear Justin: Thanks so much for your effort and information. Perhaps I did not set the proper value for vdw_switch. I will try some value. I really appreciate your nice help! On Mon, May 18, 2009 at 5:24 PM, Justin A. Lemkul wrote: > > Perhaps I can contribute something else that might be a bit more useful. > It just occurred to me that if you are only changing the vdwtype parameter, > then you are not correctly implementing the shift function. See here for > proper use of a shift potential: > > http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#vdw > > Take note of the necessary changes to vdw_shift, and potentially rlist. A > few quick tests of the shift function indicate the following: > > Case 1. Plain cutoff's at 1.2 nm > Density: 988 kg/m^3 > > Case 2. Shift potential (no other changes, i.e. rvdw_switch = 0, rvdw = > 1.2) > Density: 962 kg/m^3 > > Case 3. More appropriate shift potential (rvdw_switch = 1.0, rvdw = 1.2) > Density: 983 kg/m^3 > > -Justin > > > Justin A. Lemkul wrote: > >> >> >> Yanmei Song wrote: >> >>> Dear Justin: >>> >>> Yes and I tried dispersion correction and it gives a larger density than >>> I expected. The density of the polymer by vdwtype=shift is more close to >>> the experimental value. Then your suggestion would be to choose the >>> vdwtype=cut-off under this condition even if it result in larger density? >>> Thank you so much! >>> >>> >> No. My suggestion is to do your homework, as Mark originally said, and as >> I echoed in my last mail. Read about the water model, its expected >> performance under different simulation parameters, and evaluate what you >> want to do once you have done this background work. If you have done a >> thorough literature review, there is no one else that can make a choice for >> you; decide how to handle your system based on what you read. >> >> -Justin >> >> On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote: >>> >>> >>> >>>Yanmei Song wrote: >>> >>>Dear Justin: >>> >>>Yes. Before I do the water+polymer, I did both the bulk systems >>>separately. The density of TIP5P I mentioned earlier is the >>>results for pure water bulk system. My concern is that if it is >>>reasonable that the property of the system changes with >>>different mdp conditions? Since when I did the bulk water and >>>bulk polymer system, I found the densities change with different >>>cutoff and vdwtype conditions. Is this a artifact? Or the larger >>>cutoff, the more accurate result we can get? >>> >>> >>>Every parameter you specify will affect the results you see. I >>>agree with Mark - look up the original reference for TIP5P and see >>>what parameters are recommended. Also read the subsequent >>>literature that has used TIP5P to see what modifications >>>(electrostatic treatment, vdW treatment, etc) are appropriate or >>>even more accurate. >>> >>>Also realize that using vdwtype = shift may not be the best >>>solution. I only suggested as a guess for something to try back >>>when you were getting bizarre results with your polymer. Have you >>>ever tried dispersion correction when using vdwtype = cutoff? I >>>routinely use such a setup and have never seen any really bizarre >>>behavior. >>> >>>-Justin >>> >>>On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul >>>mailto:jalem...@vt.edu> >>><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >>> >>> >>> >>> Yanmei Song wrote: >>> >>> Dear Mark: >>> >>> Thanks for your answer. I have to use the same mdp file >>>for both >>> water and another polymer molecules in my system, right? >>> Then >>> if the shift function works well for the polymer, I can >>>not get >>> the best result for TIP5P? The density of TIP5P is >>> different >>> from the literature value of 982. Thanks! >>> >>> >>> So your system is water + polymer? In that case, you have an >>>added >>> variab
Re: [gmx-users] shift function for vdwtype and density
Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger density? Thank you so much! On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Yes. Before I do the water+polymer, I did both the bulk systems >> separately. The density of TIP5P I mentioned earlier is the results for >> pure water bulk system. My concern is that if it is reasonable that the >> property of the system changes with different mdp conditions? Since when I >> did the bulk water and bulk polymer system, I found the densities change >> with different cutoff and vdwtype conditions. Is this a artifact? Or the >> larger cutoff, the more accurate result we can get? >> >> > Every parameter you specify will affect the results you see. I agree with > Mark - look up the original reference for TIP5P and see what parameters are > recommended. Also read the subsequent literature that has used TIP5P to see > what modifications (electrostatic treatment, vdW treatment, etc) are > appropriate or even more accurate. > > Also realize that using vdwtype = shift may not be the best solution. I > only suggested as a guess for something to try back when you were getting > bizarre results with your polymer. Have you ever tried dispersion > correction when using vdwtype = cutoff? I routinely use such a setup and > have never seen any really bizarre behavior. > > -Justin > > On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Yanmei Song wrote: >> >>Dear Mark: >> >>Thanks for your answer. I have to use the same mdp file for both >>water and another polymer molecules in my system, right? Then >>if the shift function works well for the polymer, I can not get >>the best result for TIP5P? The density of TIP5P is different >>from the literature value of 982. Thanks! >> >> >>So your system is water + polymer? In that case, you have an added >>variable - the interaction between the water and your polymer. What >>you should probably be more concerned with the what the bulk density >>of the whole system is. I have found that analyzing densities of >>portions of mixed systems does not give an accurate result. >> >>-Justin >> >> >>On Mon, May 18, 2009 at 3:33 PM, Mark Abraham >>mailto:mark.abra...@anu.edu.au> >><mailto:mark.abra...@anu.edu.au >><mailto:mark.abra...@anu.edu.au>>> wrote: >> >> Yanmei Song wrote: >> >> Dear All: >> >> I found when I changed the vdwtype from cut-off to shift, >> the >> density of the system decrease significantly.All the other >> setting in the mdp file remain unchanged. For example the >> density of TIP5P water drops to 962. Does it mean I can >>not use >> the shift for vdwtype? >> >> >> Maybe not. Check out the paper in which TIP5P was >>parameterized. The >> greater the extent to which your .mdp conditions differ from >>those >> conditions, the greater the likelihood that the >>parameterization is >> no longer valid. >> >> Mark >> ___ >> gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> 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/mailing_lists/users.php >> >> >> >> >>--Yanmei Song >>Ph.D. Candidate >>Department of Chemical Engi
Re: [gmx-users] shift function for vdwtype and density
Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Mark: >> >> Thanks for your answer. I have to use the same mdp file for both water and >> another polymer molecules in my system, right? Then if the shift function >> works well for the polymer, I can not get the best result for TIP5P? The >> density of TIP5P is different from the literature value of 982. Thanks! >> > > So your system is water + polymer? In that case, you have an added > variable - the interaction between the water and your polymer. What you > should probably be more concerned with the what the bulk density of the > whole system is. I have found that analyzing densities of portions of mixed > systems does not give an accurate result. > > -Justin > > >> On Mon, May 18, 2009 at 3:33 PM, Mark Abraham >> > mark.abra...@anu.edu.au>> wrote: >> >>Yanmei Song wrote: >> >>Dear All: >> >>I found when I changed the vdwtype from cut-off to shift, the >>density of the system decrease significantly.All the other >>setting in the mdp file remain unchanged. For example the >>density of TIP5P water drops to 962. Does it mean I can not use >>the shift for vdwtype? >> >> >>Maybe not. Check out the paper in which TIP5P was parameterized. The >>greater the extent to which your .mdp conditions differ from those >>conditions, the greater the likelihood that the parameterization is >>no longer valid. >> >>Mark >>___ >>gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-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 >><mailto:gmx-users-requ...@gromacs.org>. >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> >> >> >> ___ >> 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 >> > > -- > > > 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://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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] shift function for vdwtype and density
Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! On Mon, May 18, 2009 at 3:33 PM, Mark Abraham wrote: > Yanmei Song wrote: > >> Dear All: >> >> I found when I changed the vdwtype from cut-off to shift, the density of >> the system decrease significantly.All the other setting in the mdp file >> remain unchanged. For example the density of TIP5P water drops to 962. Does >> it mean I can not use the shift for vdwtype? >> > > Maybe not. Check out the paper in which TIP5P was parameterized. The > greater the extent to which your .mdp conditions differ from those > conditions, the greater the likelihood that the parameterization is no > longer valid. > > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] shift function for vdwtype and density
Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] Re: parameter of RB potential for OPLS force field
Dear Justin: Thanks for your response. I saw this in the ffoplsaabon.itp, which I think is a Periodic potential. [ dihedraltypes ] ; ijkl func coefficients ; Added DvdS for Quartz simulations SI OS1 0.000 3.766 3 SI OH1 0.000 3.766 3 Does this mean that we can still use a periodic potential combined with OPLS force field since it seems OPLS also consists of the periodic potential besides RB. It doesn't have to be necessary to use RB for the proper dihedral when you use OPLS force field, right? Thank you so much for your help! On Fri, May 15, 2009 at 6:37 PM, Justin A. Lemkul wrote: > > There is a periodic dihedral within ffoplsaabon.itp which points to a > reference. Perhaps these are the parameters you are referring to. If not, > check out the bottom of ffoplsaabon.itp and read that paper to see if the > parameters will suit your needs. > > If you need an R-B dihedral, you may have to parameterize it yourself; not > an easy task. > > -Justin > > Yanmei Song wrote: > >> They are CH3-SI-O-SI, SI-O-SI-CH3 and SI-O-SI-O. I have looked up >> ffoplsaabon.itp. it doesn't include any dihedral consisting of SI. And the >> literatures only have the parameters for periodic potential. Thank you so >> much for your kind help! >> >> On Fri, May 15, 2009 at 4:00 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Yanmei Song wrote: >> >>Yes, I have read that part and still have no idea how can I do >>that. That part tells us how to transfer from the OPLS >>parameters Vi to RB potential in GROMOS force field Ci. Now >>what I have is phi and k for periodic potential. Is there any >>way I can get Ci for RB potential from phi and k in order to use >>OPLS force field? >> >> >>I don't know if there is a direct conversion. There are, however, >>over 1000 existing dihedrals in ffoplsaabon.itp; which dihedral are >>you looking for that you can't find? >> >>-Justin >> >>On Fri, May 15, 2009 at 3:34 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> Please keep all Gromacs-related correspondence on the gmx-users >> list. That way, the discussion is archived for the later >>benefit of >> others, and you have a chance to reach a wider audience of >> individuals who may be able to help you. >> >> That said, read the manual, section 4.2.12. >> >> -Justin >> >> >> Yanmei Song wrote: >> >> Dear Justin: >> >> If I have the parameters of GROMOS force field for the >> proper >> dihedral, which i think they are phi and k for function 1 >> for >> periodic type. I wanted to use OPLS force field. As far as I >> know in OPLS the dihedral was RB potential in fuction 3. >>So my >> question is do you know any method I can transfer this >>parameter >> to RB parameters? Or these two potentials have no >>connections? >> Thanks >> >> --Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> >> --======== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >>231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ==== >> >> >> >> >>--Yanmei Song >>Ph.D. Candidate >>Department of Chemical Engineering >>Arizona State University >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >>http://www.bevanlab.biochem.vt
[gmx-users] Re: parameter of RB potential for OPLS force field
They are CH3-SI-O-SI, SI-O-SI-CH3 and SI-O-SI-O. I have looked up ffoplsaabon.itp. it doesn't include any dihedral consisting of SI. And the literatures only have the parameters for periodic potential. Thank you so much for your kind help! On Fri, May 15, 2009 at 4:00 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Yes, I have read that part and still have no idea how can I do that. That >> part tells us how to transfer from the OPLS parameters Vi to RB potential in >> GROMOS force field Ci. Now what I have is phi and k for periodic potential. >> Is there any way I can get Ci for RB potential from phi and k in order to >> use OPLS force field? >> >> > I don't know if there is a direct conversion. There are, however, over > 1000 existing dihedrals in ffoplsaabon.itp; which dihedral are you looking > for that you can't find? > > -Justin > > On Fri, May 15, 2009 at 3:34 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >>Please keep all Gromacs-related correspondence on the gmx-users >>list. That way, the discussion is archived for the later benefit of >>others, and you have a chance to reach a wider audience of >> individuals who may be able to help you. >> >>That said, read the manual, section 4.2.12. >> >>-Justin >> >> >>Yanmei Song wrote: >> >>Dear Justin: >> >>If I have the parameters of GROMOS force field for the proper >>dihedral, which i think they are phi and k for function 1 for >>periodic type. I wanted to use OPLS force field. As far as I >>know in OPLS the dihedral was RB potential in fuction 3. So my >>question is do you know any method I can transfer this parameter >>to RB parameters? Or these two potentials have no connections? >>Thanks >> >>--Yanmei Song >>Ph.D. Candidate >>Department of Chemical Engineering >>Arizona State University >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>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 >> >> >> >> >> >> >> -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> > > -- > > > 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 > > > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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: parameter of RB potential for OPLS force field
Yes, I have read that part and still have no idea how can I do that. That part tells us how to transfer from the OPLS parameters Vi to RB potential in GROMOS force field Ci. Now what I have is phi and k for periodic potential. Is there any way I can get Ci for RB potential from phi and k in order to use OPLS force field? On Fri, May 15, 2009 at 3:34 PM, Justin A. Lemkul wrote: > > Please keep all Gromacs-related correspondence on the gmx-users list. That > way, the discussion is archived for the later benefit of others, and you > have a chance to reach a wider audience of individuals who may be able to > help you. > > That said, read the manual, section 4.2.12. > > -Justin > > > Yanmei Song wrote: > >> Dear Justin: >> >> If I have the parameters of GROMOS force field for the proper dihedral, >> which i think they are phi and k for function 1 for periodic type. I wanted >> to use OPLS force field. As far as I know in OPLS the dihedral was RB >> potential in fuction 3. So my question is do you know any method I can >> transfer this parameter to RB parameters? Or these two potentials have no >> connections? Thanks >> >> -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> > > -- > > > 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 > > > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] parameter of RB potential for OPLS force field
Dear Justin: If I have the parameters of GROMOS force field for the proper dihedral, which i think they are phi and k for function 1 for periodic type. I wanted to use OPLS force field. As far as I know in OPLS the dihedral was RB potential in fuction 3. So my question is do you know any method I can transfer this parameter to RB parameters? Or these two potentials have no connections? Thanks -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] Pressure coupling and cut-off
Dear Justin: Thank you for your suggestions. using shift for vdwtype helps a lot. Can I ask you another question? The density of my system is about 8% larger than the experimental value. Do you have any suggestions on how to reduce the density of the system. Or once the force field and all the parameters are fixed, the density is independent of the MD procedure? I am using NPT ensemble with the mdp I mentioned before with added vdwtype = shift. On Thu, May 14, 2009 at 4:35 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Thanks for your response. Here is the complete my .mdp file: >> >> title = pdm >> cpp = /lib/cpp >> constraints = all_bonds >> integrator = md >> dt = 0.004 ; ps ! >> nsteps = 250 ; total 10ns. >> nstcomm = 1 >> nstxout = 5 >> nstvout = 5 >> nstfout = 0 >> nstlog = 5000 >> nstenergy = 5000 >> nstxtcout = 25000 >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> coulombtype = PME >> rlist = 1.4 >> rcoulomb= 1.4 >> rvdw= 1.4 >> fourierspacing = 0.20 >> pme_order = 4 >> ewald_rtol = 1e-5 >> ; Berendsen temperature coupling is on in one groups >> Tcoupl = berendsen >> tc_grps = PDM >> tau_t = 0.1 >> ref_t = 300 >> ; Energy monitoring >> energygrps = PDM >> ; Isotropic pressure coupling is now on >> Pcoupl = berendsen >> pcoupltype = isotropic >> ;pc-grps= PDM >> tau_p = 1.0 >> ref_p = 1.0 >> compressibility = 4.5e-5 >> >> ; Generate velocites is off at 300 K. >> gen_vel = yes >> gen_temp= 300.0 >> gen_seed= 10 >> >> >> > The problem you're seeing could be an artifact of the shorter cutoff. Have > you tried using DispCorr = EnerPres? Or what about using a Shift function > for vdwtype? You might see better energy conservation in that case compared > to a plain cutoff. > > -Justin > > >> On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Yanmei Song wrote: >> >>Dear All: >> >>I have question about the pressure coupling. I have done a 10ns >>simulation with 19800 atoms for 120 large molecules using the >>following pressure coupling. >> >>Tcoupl = berendsen >>tc_grps = PDM >>tau_t = 0.1 >>ref_t = 300 >> >>Pcoupl = berendsen >>pcoupltype = isotropic >>;pc-grps= PDM >>tau_p = 1.0 >>ref_p = 1.0 >>compressibility = 4.5e-5 >> >>Then I did g_energy for the last 3ns and got the results: >> >>Energy Average RMSD Fluct. >> Drift Tot-Drift >> >> >> --- >>Potential-98061 0 0 >> 0.616681850.04 >>Temperature 303.561109.602109.602 >>0.000181791 0.545372 >>Pressure (bar) 4.48840.811109.8 >> -0.169835 -509.506 >> >>For such a long run the pressure drift is still too much and >>seem hasn't approached 1bar. Does it mean the system hasn't >>reach equilibrium yet. I did a similar system by using the same >>method. it just take 2 or 3ns to reach the equilibrium. and the >>pressure is around 1.01after the run. The only difference is the >>cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too >>large to make the system running slower. Or the pressure >>coupling method is not working well. Anyone can give me any >>suggestions? >> >> >> >>I think it will depend on the interplay of other parameters as well. >> Posting a complete .mdp file may be more helpful. >> >>-Justin >> >>--Y
Re: [gmx-users] Pressure coupling and cut-off
Dear Justin: Thanks for your response. Here is the complete my .mdp file: title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 250 ; total 10ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 fourierspacing = 0.20 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in one groups Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = PDM ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear All: >> >> I have question about the pressure coupling. I have done a 10ns simulation >> with 19800 atoms for 120 large molecules using the following pressure >> coupling. >> >> Tcoupl = berendsen >> tc_grps = PDM >> tau_t = 0.1 >> ref_t = 300 >> >> Pcoupl = berendsen >> pcoupltype = isotropic >> ;pc-grps= PDM >> tau_p = 1.0 >> ref_p = 1.0 >> compressibility = 4.5e-5 >> >> Then I did g_energy for the last 3ns and got the results: >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> >> --- >> Potential-98061 0 00.61668 >> 1850.04 >> Temperature 303.561109.602109.602 0.000181791 >> 0.545372 >> Pressure (bar) 4.48840.811109.8 -0.169835 >> -509.506 >> >> For such a long run the pressure drift is still too much and seem hasn't >> approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did >> a similar system by using the same method. it just take 2 or 3ns to reach >> the equilibrium. and the pressure is around 1.01after the run. The only >> difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 >> is too large to make the system running slower. Or the pressure coupling >> method is not working well. Anyone can give me any suggestions? >> >> >> > I think it will depend on the interplay of other parameters as well. > Posting a complete .mdp file may be more helpful. > > -Justin > > -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> >> >> >> ___ >> 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 >> > > -- > > > 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://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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] Pressure coupling and cut-off
Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 Then I did g_energy for the last 3ns and got the results: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential-98061 0 00.61668 1850.04 Temperature 303.561109.602109.602 0.000181791 0.545372 Pressure (bar) 4.48840.811109.8 -0.169835 -509.506 For such a long run the pressure drift is still too much and seem hasn't approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did a similar system by using the same method. it just take 2 or 3ns to reach the equilibrium. and the pressure is around 1.01after the run. The only difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too large to make the system running slower. Or the pressure coupling method is not working well. Anyone can give me any suggestions? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] Some molecules disconnected into many parts after EM
Dear Justin: - Program mdrun_d, VERSION 4.0.4 Source code file: gmx_fft_mkl.c, line: 825 Fatal error: Error executing Intel MKL FFT. --- I really could not find out what is the reason for the error above. Do you mean something is wrong with the installation. if this is the case then should I re-install it? This morning I did the same procedure with the same input file using gromacs-3.3.3 ( which means I did all the editconf, genbox EM, and mdrun in 3.3.3) and the mdrun works well. So I think there must be something wrong with the 4.0.4. How can I fix this? Anyone had the same problem before? On Fri, May 8, 2009 at 1:04 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Sorry to bother so many times. After EM everything looks fine. However the >> mdrun died with the error: >> >> --- >> Program mdrun_d, VERSION 4.0.4 >> Source code file: gmx_fft_mkl.c, line: 825 >> >> Fatal error: >> Error executing Intel MKL FFT. >> --- >> >> what is the problem coming from? >> >> > It looks like you have Intel MKL for your FFT package, but mdrun can't find > it (or it otherwise failed for some reason). Make sure your environment can > find the location of all necessary binaries or libraries and try again. > > -Justin > > On Fri, May 8, 2009 at 11:28 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >>VMD guesses bonds based on distances, so it is not necessarily very >>smart. >> >>I have no idea why increasing the box causes the molecules to be >>displayed correctly, other than that VMD cannot deal with the >>periodicity correctly, as I implied before. Causing all of the >>molecules to be within the unit cell may lead VMD to induce the >>desired visualization. >> >>But in any case, bonds aren't broken and/or formed in classical MD >>so there is likely nothing to be concerned about. >> >>-Justin >> >>Yanmei Song wrote: >> >>Dear Justin: >> >>Thanks for your message. >> >>When I open the gro file using VMD it shows: >> >>atom:1950 >>bonds 1907 >>residue:43 >> >>I was thinking the problem may not come from the artifact of >>visualization. Since if the gro file is fine it should be like: >> >>atom:1950 >>bonds 1944 >>residue:6 >> >>because I have 6 chains in the box. >> >>This morning I found that it seems the problem was resolved by >>increasing the box size. Why is that? >> >> >>On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Yanmei Song wrote: >> >> Dear users: >> >> I set up a 8nm cubic box with 6 long chain molecules. >>After EM, >> there is no error message. However I found that in the >>gro file >> by visualization, 2 of the chains has been split in many >>parts, >> which means many bonds in the molecules disconnected. And >>also >> the other 4 are good. I checked em.log and eveyting looks >>fine. >> >> Steepest Descents converged to machine precision in 1545 >>steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -7.51461594735782e+03 >> Maximum force = 2.66505909651672e+02 on atom 1256 >> Norm of force = 9.84300153087768e+00 >> >> Anyone knows how to solve the problem? Thanks in advance! >> >> >> Probably an artifact of visualization, or otherwise periodic >> boundary conditions: >> >> http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions >> >> -Justin >> >> --Yanmei Song >> Department of Chemical Engineering >> ASU >> >> >> >> >> >> ___ >>
Re: [gmx-users] Some molecules disconnected into many parts after EM
Dear Justin: Sorry to bother so many times. After EM everything looks fine. However the mdrun died with the error: --- Program mdrun_d, VERSION 4.0.4 Source code file: gmx_fft_mkl.c, line: 825 Fatal error: Error executing Intel MKL FFT. --- what is the problem coming from? On Fri, May 8, 2009 at 11:28 AM, Justin A. Lemkul wrote: > > VMD guesses bonds based on distances, so it is not necessarily very smart. > > I have no idea why increasing the box causes the molecules to be displayed > correctly, other than that VMD cannot deal with the periodicity correctly, > as I implied before. Causing all of the molecules to be within the unit > cell may lead VMD to induce the desired visualization. > > But in any case, bonds aren't broken and/or formed in classical MD so there > is likely nothing to be concerned about. > > -Justin > > Yanmei Song wrote: > >> Dear Justin: >> >> Thanks for your message. >> >> When I open the gro file using VMD it shows: >> >> atom:1950 >> bonds 1907 >> residue:43 >> >> I was thinking the problem may not come from the artifact of >> visualization. Since if the gro file is fine it should be like: >> >> atom:1950 >> bonds 1944 >> residue:6 >> >> because I have 6 chains in the box. >> >> This morning I found that it seems the problem was resolved by increasing >> the box size. Why is that? >> >> >> On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Yanmei Song wrote: >> >>Dear users: >> >>I set up a 8nm cubic box with 6 long chain molecules. After EM, >>there is no error message. However I found that in the gro file >>by visualization, 2 of the chains has been split in many parts, >>which means many bonds in the molecules disconnected. And also >>the other 4 are good. I checked em.log and eveyting looks fine. >> >>Steepest Descents converged to machine precision in 1545 steps, >>but did not reach the requested Fmax < 10. >>Potential Energy = -7.51461594735782e+03 >>Maximum force = 2.66505909651672e+02 on atom 1256 >>Norm of force = 9.84300153087768e+00 >> >>Anyone knows how to solve the problem? Thanks in advance! >> >> >>Probably an artifact of visualization, or otherwise periodic >>boundary conditions: >> >>http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions >> >>-Justin >> >>--Yanmei Song >>Department of Chemical Engineering >>ASU >> >> >> >> >> >>___ >>gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-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 >><mailto: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 <http://vt.edu> | (540) 231-9080 >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ==== >>___ >>gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-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 >><mailto:gmx-users-requ...@gromacs.org>. >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Yanmei Song >> Department of Chemical Engineering
Re: [gmx-users] Some molecules disconnected into many parts after EM
Dear Justin: Thanks for your message. When I open the gro file using VMD it shows: atom:1950 bonds 1907 residue:43 I was thinking the problem may not come from the artifact of visualization. Since if the gro file is fine it should be like: atom:1950 bonds 1944 residue:6 because I have 6 chains in the box. This morning I found that it seems the problem was resolved by increasing the box size. Why is that? On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear users: >> >> I set up a 8nm cubic box with 6 long chain molecules. After EM, there is >> no error message. However I found that in the gro file by visualization, 2 >> of the chains has been split in many parts, which means many bonds in the >> molecules disconnected. And also the other 4 are good. I checked em.log and >> eveyting looks fine. >> >> Steepest Descents converged to machine precision in 1545 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -7.51461594735782e+03 >> Maximum force = 2.66505909651672e+02 on atom 1256 >> Norm of force = 9.84300153087768e+00 >> >> Anyone knows how to solve the problem? Thanks in advance! >> >> > Probably an artifact of visualization, or otherwise periodic boundary > conditions: > > http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions > > -Justin > > -- >> Yanmei Song >> Department of Chemical Engineering >> ASU >> >> >> >> >> ___ >> 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 >> > > -- > > > 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://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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Some molecules disconnected into many parts after EM
Dear users: I set up a 8nm cubic box with 6 long chain molecules. After EM, there is no error message. However I found that in the gro file by visualization, 2 of the chains has been split in many parts, which means many bonds in the molecules disconnected. And also the other 4 are good. I checked em.log and eveyting looks fine. Steepest Descents converged to machine precision in 1545 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.51461594735782e+03 Maximum force = 2.66505909651672e+02 on atom 1256 Norm of force = 9.84300153087768e+00 Anyone knows how to solve the problem? Thanks in advance! -- Yanmei Song Department of Chemical Engineering ASU ___ 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 set up the cut-off radius
Dear All: I am working on a large polymer molecule system. The single molecules has a dimension of 5nm. My question is how can I set up the cut-off in my md.mdp. I tried the cut-off of 1.2 and got the following two notes: NOTE 1 [file md.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. processing topology... Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.itp Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaanb.itp Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'PDM' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat There are: 6 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... Making dummy/rest group for Acceleration containing 1950 elements Making dummy/rest group for Freeze containing 1950 elements Making dummy/rest group for VCM containing 1950 elements Number of degrees of freedom in T-Coupling group PDM is 3903.00 Making dummy/rest group for User1 containing 1950 elements Making dummy/rest group for User2 containing 1950 elements Making dummy/rest group for XTC containing 1950 elements Making dummy/rest group for Or. Res. Fit containing 1950 elements Making dummy/rest group for QMMM containing 1950 elements T-Coupling has 1 element(s): PDM Energy Mon. has 1 element(s): PDM Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 56x63x65, spacing 0.118 0.116 0.119 Estimate for the relative computational load of the PME mesh part: 0.90 NOTE 2 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 3 Mb of data writing run input file... *#1: For the note 1, do I have to change to V-rescale thermostat. since I used Berendsen for my prior systems and i want to be consistent. #2: How large should the cut-off be? Do I have to set up the cut-off to be larger than the dimension of the single molecule? Thank you so much for your help in advance!* -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Energy minimization error by GMX 4.0.4
Thank you so much for all the helpful response. On Wed, May 6, 2009 at 4:59 PM, Mark Abraham wrote: > Yanmei Song wrote: > >> Dear All: >> >> I just installed the gmx_4.0.4 double precision. >> >> When I do EM, the grompp_d command has no problem. However after I submit >> the job, it gives me the following error. Anyone can tell me what is the >> problem which may cause that? >> > > You're using a new .tpr with an old mdrun. > > By the way, in 4.0.4, it can only use 4 CPU, right? >> > > No. > > Can we still specify how much CPU we want to use by -np? >> > > As an argument to mdrun yes, as an argument to grompp, no. > > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU ___ 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: Energy minimization error by GMX 4.0.4
Also I have checked that it works well in gmx_3.3.3. Anyone can tell me what is the problem ? Thanks! On Wed, May 6, 2009 at 1:47 PM, Yanmei Song wrote: > Dear All: > > I just installed the gmx_4.0.4 double precision. > > When I do EM, the grompp_d command has no problem. However after I submit > the job, it gives me the following error. Anyone can tell me what is the > problem which may cause that? By the way, in 4.0.4, it can only use 4 CPU, > right? Can we still specify how much CPU we want to use by -np? > > Reading file /home/ysong30/pdm80/em.tpr, VERSION 4.0.4 (double precision) > > --- > Program mdrun, VERSION 3.3.3 > Source code file: tpxio.c, line: 1192 > > Fatal error: > reading tpx file (/home/ysong30/pdm80/em.tpr) version 58 with version 40 > program > > > -- > Yanmei Song > Department of Chemical Engineering > ASU > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Energy minimization error by GMX 4.0.4
Dear All: I just installed the gmx_4.0.4 double precision. When I do EM, the grompp_d command has no problem. However after I submit the job, it gives me the following error. Anyone can tell me what is the problem which may cause that? By the way, in 4.0.4, it can only use 4 CPU, right? Can we still specify how much CPU we want to use by -np? Reading file /home/ysong30/pdm80/em.tpr, VERSION 4.0.4 (double precision) --- Program mdrun, VERSION 3.3.3 Source code file: tpxio.c, line: 1192 Fatal error: reading tpx file (/home/ysong30/pdm80/em.tpr) version 58 with version 40 program -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Error by pdb2gmx
Dear Mark:
This error is being provoked at the top of the .rtp file when a line with
something like "[header]" is not parsing suitably. A while ago I suggested
using diff on the .rtp file. Do that.
Would you mind telling me how to do that in detail?
I tried the following and it doesn't work.
diff
[ PDM ]
; designation arbitrary, C1 and C2 is -CH3
[ atoms ]
SI1 SI 0.3001
C1 opls_069 0.0001
C2 opls_069 0.0001
O1 opls_108-0.3001
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1
; Terminal PDMS residue ("beginning" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDMB ]
[ atoms ]
C1opls_069 0.0001
SI1SI 0.3001
C2opls_069 0.0001
C3opls_069 0.0001
O1opls_108-0.3001
[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1
; Terminal PE residue ("end" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDME ]
[ atoms ]
SI1SI 0.0001
C1opls_069 0.0001
C2opls_069 0.0001
C3opls_069 0.0001
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3
diff
Thanks a lot in advance!
On Mon, May 4, 2009 at 10:15 PM, Mark Abraham
wrote:
> Justin A. Lemkul wrote:
>>
>> Then it seems clear to me that your installation of Gromacs is faulty.
>> Have you tried running the test set (available on the wiki site)? If
you
>> can describe your computer system (OS, version, compilers used,
>> configuration options, etc.) then perhaps someone on the list can spot a
>> potential pitfall.
>>
>> -Justin
>>
>> Yanmei Song wrote:
>>>
>>> Dear Justin:
>>>
>>> Thank you so much for your help earlier. I updated my GROMACS to
>>> 4.0.4. When I run pdb2gmx using the following two files. I still got
>>> the similar error message:
>>>
>>> Opening library file ffoplsaa.rtp
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
>>> WARNING: masses will be determined based on residue and atom names,
>>> this can deviate from the real mass of the atom type
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
>>> Entries in atommass.dat: 178
>>> WARNING: vdwradii will be determined based on residue and atom names,
>>> this can deviate from the real mass of the atom type
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
>>> Entries in vdwradii.dat: 28
>>> Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
>>> Entries in dgsolv.dat: 7
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
>>> Entries in electroneg.dat: 71
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/elements.dat
>>> Entries in elements.dat: 218
>>> Reading pdms2.pdb...
>>> Read 13 atoms
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat
>>> 26 out of 26 lines of xlateat.dat converted succesfully
>>> Analyzing pdb file
>>> There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
>>>
>>> chain #res #atoms
>>> 1 ' ' 3 13
>>>
>>> All occupancies are one
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
>>> Atomtype 1
>>> Reading residue database... (ffoplsaa)
>>> Opening library file ffoplsaa.rtp
>>>
>>> ---
>>> Program pdb2gmx_d, VERSION 4.0.4
>>> Source code file: resall.c, line: 279
>>>
>>> Fatal error:
>>> in .rtp file at line:
>>>
>>>
>>> ---
>
> This error is being provoked at the top of the .rtp file when a line with
> something like "[header]" is not parsing suitably. A while ago I suggested
> using diff on the .rtp file. Do that.
>
> 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 gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Yanmei Song
Department of Chemical Engineering
ASU
___
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] Error by pdb2gmx
Dear Justin:
Thank you so much for your help earlier. I updated my GROMACS to
4.0.4. When I run pdb2gmx using the following two files. I still got
the similar error message:
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
chain #res #atoms
1 ' ' 3 13
All occupancies are one
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
---
Program pdb2gmx_d, VERSION 4.0.4
Source code file: resall.c, line: 279
Fatal error:
in .rtp file at line:
---
My new residue added to ffoplass.rtp is:
[ PDM ]
; designation arbitrary, C1 and C2 is -CH3
[ atoms ]
SI1 SI 0.3001
C1 opls_069 0.0001
C2 opls_069 0.0001
O1 opls_108-0.3001
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1
; Terminal PDMS residue ("beginning" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDMB ]
[ atoms ]
C1opls_069 0.0001
SI1SI 0.3001
C2opls_069 0.0001
C3opls_069 0.0001
O1opls_108-0.3001
[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1
; Terminal PE residue ("end" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDME ]
[ atoms ]
SI1SI 0.0001
C1opls_069 0.0001
C2opls_069 0.0001
C3opls_069 0.0001
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3
PDB file:
ATOM 1 SI1 PDMB1 8.995 -3.779 -2.091 1.00 0.00
ATOM 2 C1 PDMB1 10.682 -3.453 -2.828 1.00 0.00
ATOM 3 C2 PDMB1 8.020 -2.184 -2.039 1.00 0.00
ATOM 4 O1 PDMB1 8.142 -4.958 -3.082 1.00 0.00
ATOM 5 C3 PDMB1 9.192 -4.446 -0.356 1.00 0.00
ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
ATOM 10 SI1 PDME3 6.370 -8.062 -6.022 1.00 0.00
ATOM 11 C1 PDME3 7.679 -8.351 -7.325 1.00 0.00
ATOM 12 C2 PDME3 5.990 -9.673 -5.153 1.00 0.00
ATOM 13 C3 PDME3 4.816 -7.411 -6.834 1.00 0.00
TER
Thanks a lot!
On Thu, Apr 30, 2009 at 5:04 PM, Justin A. Lemkul wrote:
>
> Your system works for me under Gromacs 4.0.4 - the only issue is that your
> PDME residue has a net +0.3 charge. Does your Gromacs installation work
> properly for proven systems like proteins?
>
> I would suggest upgrading to version 4.0.4 and trying again. If that does
> not work, post to the list a complete description of your hardware and
> software - OS, version, compilers used, configuration options, etc, and see
> if anyone can spot a problem.
>
> -Justin
>
> Yanmei Song wrote:
>>
>> Sorry to bother so many times.
>>
>> I edited the rtp and added the new residue as following, which I think
>> should be no problem.
>>
>> [ PDM ]
>>
>> [ atoms ]
>> SI1 SI 0.300 1
>> C1 opls_069 0.000 1
>> C2 opls_069 0.000 1
>> O1 opls_108 -0.300 1
>>
>> [ bonds ]
>> SI1 -O1
>> SI1 C1
>> SI1 C2
>> SI1 O1
>> O1 +SI1
>>
>>
>> ; Terminal PDMS residue ("beginning
Re: [gmx-users] Error by pdb2gmx
That means both the rtp and pdb files work in your GROMACS-4.0.4. For
the issue of" PDME residue has a net +0.3 charge" , I should change
the charge to 0 for Si in PDME, which I have ignored. I will update
the software and see if it works. Thanks so much for your help!
On Thu, Apr 30, 2009 at 5:04 PM, Justin A. Lemkul wrote:
>
> Your system works for me under Gromacs 4.0.4 - the only issue is that your
> PDME residue has a net +0.3 charge. Does your Gromacs installation work
> properly for proven systems like proteins?
>
> I would suggest upgrading to version 4.0.4 and trying again. If that does
> not work, post to the list a complete description of your hardware and
> software - OS, version, compilers used, configuration options, etc, and see
> if anyone can spot a problem.
>
> -Justin
>
> Yanmei Song wrote:
>>
>> Sorry to bother so many times.
>>
>> I edited the rtp and added the new residue as following, which I think
>> should be no problem.
>>
>> [ PDM ]
>>
>> [ atoms ]
>> SI1 SI 0.300 1
>> C1 opls_069 0.000 1
>> C2 opls_069 0.000 1
>> O1 opls_108 -0.300 1
>>
>> [ bonds ]
>> SI1 -O1
>> SI1 C1
>> SI1 C2
>> SI1 O1
>> O1 +SI1
>>
>>
>> ; Terminal PDMS residue ("beginning" of chain)
>>
>> [ PDMB ]
>> [ atoms ]
>> C1 opls_069 0.000 1
>> SI1 SI 0.300 1
>> C2 opls_069 0.000 1
>> C3 opls_069 0.000 1
>> O1 opls_108 -0.300 1
>>
>> [ bonds ]
>> SI1 C1
>> SI1 C2
>> SI1 C3
>> SI1 O1
>> O1 +SI1
>>
>>
>> ; Terminal PDMS residue ("end" of chain)
>>
>>
>> [ PDME ]
>> [ atoms ]
>> SI1 SI 0.300 1
>> C1 opls_069 0.000 1
>> C2 opls_069 0.000 1
>> C3 opls_069 0.000 1
>>
>> [ bonds ]
>> SI1 -O1
>> SI1 C1
>> SI1 C2
>> SI1 C3
>>
>> Also my pdb is :
>>
>> ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00
>> ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00
>> ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00
>> ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00
>> ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00
>> ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
>> ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
>> ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
>> ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
>> ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00
>> ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00
>> ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00
>> ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00
>> TER
>>
>> after pdb2gmx, I still got the error:
>>
>> Opening library file ffoplsaa.rtp
>> Opening library file
>> /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
>> Reading pdms2.pdb...
>> Read 13 atoms
>> Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
>> 26 out of 26 lines of xlateat.dat converted succesfully
>> Analyzing pdb file
>> There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
>>
>> chain #res #atoms
>> 1 ' ' 3 13
>>
>> All occupancies are one
>> Opening library file
>> /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
>> Atomtype 817
>> Reading residue database... (ffoplsaa)
>> Opening library file ffoplsaa.rtp
>>
>> ---
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: resall.c, line: 289
>>
>> Fatal error:
>> in .rtp file at line:
>>
>>
>> ---
>>
>> Anyone knows where I did wrong?
>>
>> Thank you so much!
>> On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul
>> wrote:
>>>
>>> Yanmei Song wrote:
>>>>
>>>> Hi, Dallas:
>>>>
>>>> I added this to the ffoplsaa.rtp
>>>>
>>>> [ PDM ]
>>>>
>>>> [ atoms ]
>>>> SI SI 0.300 1
>>>
Re: [gmx-users] Error by pdb2gmx
Sorry to bother so many times.
I edited the rtp and added the new residue as following, which I think
should be no problem.
[ PDM ]
[ atoms ]
SI1SI 0.3001
C1 opls_069 0.0001
C2 opls_069 0.0001
O1 opls_108-0.3001
[ bonds ]
SI1 -O1
SI1C1
SI1C2
SI1O1
O1 +SI1
; Terminal PDMS residue ("beginning" of chain)
[ PDMB ]
[ atoms ]
C1opls_069 0.0001
SI1 SI 0.3001
C2opls_069 0.0001
C3opls_069 0.0001
O1opls_108-0.3001
[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1
; Terminal PDMS residue ("end" of chain)
[ PDME ]
[ atoms ]
SI1 SI 0.3001
C1opls_069 0.0001
C2opls_069 0.0001
C3opls_069 0.0001
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3
Also my pdb is :
ATOM 1 SI1 PDMB1 8.995 -3.779 -2.091 1.00 0.00
ATOM 2 C1 PDMB1 10.682 -3.453 -2.828 1.00 0.00
ATOM 3 C2 PDMB1 8.020 -2.184 -2.039 1.00 0.00
ATOM 4 O1 PDMB1 8.142 -4.958 -3.082 1.00 0.00
ATOM 5 C3 PDMB1 9.192 -4.446 -0.356 1.00 0.00
ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
ATOM 10 SI1 PDME3 6.370 -8.062 -6.022 1.00 0.00
ATOM 11 C1 PDME3 7.679 -8.351 -7.325 1.00 0.00
ATOM 12 C2 PDME3 5.990 -9.673 -5.153 1.00 0.00
ATOM 13 C3 PDME3 4.816 -7.411 -6.834 1.00 0.00
TER
after pdb2gmx, I still got the error:
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
chain #res #atoms
1 ' ' 3 13
All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
---
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
Fatal error:
in .rtp file at line:
---
Anyone knows where I did wrong?
Thank you so much!
On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul wrote:
>
>
> Yanmei Song wrote:
>>
>> Hi, Dallas:
>>
>> I added this to the ffoplsaa.rtp
>>
>> [ PDM ]
>>
>> [ atoms ]
>> SI SI 0.300 1
>> CH3 opls_069 0.000 1
>> O opls_108 -0.300 1
>>
>> [ bonds ]
>> SI O
>> SI CH3
>>
>>
>> [ dihedrals ]
>> CH3 SI O SI dih_PDM_chi1_C_SI_O_SI
>> SI O SI CH3 dih_PDM_chi1_SI_O_SI_C
>> O SI O SI dih_PDM_chi1_O_SI_O_SI
>>
>> The format is the same with other entries. Do you guys think anything
>> wrong with it?
>>
>> Also what does it mean by the error message:
>>
>> Opening library file ffoplsaa.rtp
>> Opening library file
>> /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
>> Reading pdms10.pdb...
>> Read 45 atoms
>> Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
>> 26 out of 26 lines of xlateat.dat converted succesfully
>> Analyzing pdb file
>> There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
>>
>> chain #res #atoms
>> 1 'A' 1 45
>>
>> All occupancies are one
>> Opening library file
>> /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
>> Atomtype 817
>> Reading residue database... (ffoplsaa)
>> Opening library file ffoplsaa.rtp
>>
>> ---
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: resall.c, line: 289
>>
>> Fatal error:
>> in .rtp file at line:
>>
>>
>> ---
>>
>> what is "Source code file: resall.c, line: 289" It seems the problem
>> comes from here.
>
> That is the line of code that is spotting a problem.
>
> I think the issue is that, in your original .pdb fi
Re: [gmx-users] Error by pdb2gmx
Hi, Justin: Thank you so much for your nice help. I will work on that according to your suggestions. On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: >> >> Hi, Dallas: >> >> I added this to the ffoplsaa.rtp >> >> [ PDM ] >> >> [ atoms ] >> SI SI 0.300 1 >> CH3 opls_069 0.000 1 >> O opls_108 -0.300 1 >> >> [ bonds ] >> SI O >> SI CH3 >> >> >> [ dihedrals ] >> CH3 SI O SI dih_PDM_chi1_C_SI_O_SI >> SI O SI CH3 dih_PDM_chi1_SI_O_SI_C >> O SI O SI dih_PDM_chi1_O_SI_O_SI >> >> The format is the same with other entries. Do you guys think anything >> wrong with it? >> >> Also what does it mean by the error message: >> >> Opening library file ffoplsaa.rtp >> Opening library file >> /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat >> Reading pdms10.pdb... >> Read 45 atoms >> Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat >> 26 out of 26 lines of xlateat.dat converted succesfully >> Analyzing pdb file >> There are 1 chains and 0 blocks of water and 1 residues with 45 atoms >> >> chain #res #atoms >> 1 'A' 1 45 >> >> All occupancies are one >> Opening library file >> /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp >> Atomtype 817 >> Reading residue database... (ffoplsaa) >> Opening library file ffoplsaa.rtp >> >> --- >> Program pdb2gmx, VERSION 3.3.3 >> Source code file: resall.c, line: 289 >> >> Fatal error: >> in .rtp file at line: >> >> >> --- >> >> what is "Source code file: resall.c, line: 289" It seems the problem >> comes from here. > > That is the line of code that is spotting a problem. > > I think the issue is that, in your original .pdb file, you have dozens of > atoms in your polymer chain, all labeled as residue 1. What your .rtp entry > says is that a single PDM should contain only three atoms. Since what you > are trying to do is make a building block, you will need to do several > things: > > 1. Re-number your .pdb file so that multiple monomers are apparent. > 2. Use the + and - characters to indicate connectivity to the next residue > and previous residue, respectively. > 3. Create separate .rtp entries for terminal groups, as I suggested > previously, so that termini are handled correctly (since the -n.tdb and > -c.tdb files cannot be used for non-protein). > > See the amino acid entries for examples on how to use + and - appropriately, > or the list archive for examples provided by other users for other polymers > (polyethylene is especially common), for example: > > http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html > > -Justin > >> >> Thanks a lot! >> >> >> On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren >> wrote: >>> >>> Check consistency with other entries around it, easy way to check to see >>> that you have the right format. >>> >>> What did you edit the file with? >>> >>> Catch ya, >>> >>> Dr. Dallas Warren >>> Department of Pharmaceutical Biology and Pharmacology >>> Pharmacy and Pharmaceutical Sciences, Monash University >>> 381 Royal Parade, Parkville VIC 3010 >>> dallas.war...@pharm.monash.edu.au >>> +61 3 9903 9167 >>> - >>> When the only tool you own is a hammer, every problem begins to resemble >>> a nail. >>> >>>> -Original Message- >>>> From: gmx-users-boun...@gromacs.org >>>> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >>>> Sent: Thursday, 30 April 2009 9:07 AM >>>> To: jalem...@vt.edu; Discussion list for GROMACS users >>>> Subject: Re: [gmx-users] Error by pdb2gmx >>>> >>>> This is the new entry I added to the rtp file. >>>> >>>> [ PDM ] >>>> >>>> >>>> [ atoms ] >>>> SI SI 0.300 1 >>>> CH3 opls_069 0.000 1 >>>> O opls_108 -0.300 1 >>>> >>>> >>>> [ bonds ] >>>> SI O 0.190 158805.0 >>>> SI CH3 0.164 293
Re: [gmx-users] Error by pdb2gmx
Hi, Dallas: I added this to the ffoplsaa.rtp [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O SI CH3 [ dihedrals ] CH3SIO SI dih_PDM_chi1_C_SI_O_SI SI O SI CH3 dih_PDM_chi1_SI_O_SI_C OSIO SI dih_PDM_chi1_O_SI_O_SI The format is the same with other entries. Do you guys think anything wrong with it? Also what does it mean by the error message: Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat Reading pdms10.pdb... Read 45 atoms Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 45 atoms chain #res #atoms 1 'A' 1 45 All occupancies are one Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- what is "Source code file: resall.c, line: 289" It seems the problem comes from here. Thanks a lot! On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren wrote: > Check consistency with other entries around it, easy way to check to see that > you have the right format. > > What did you edit the file with? > > Catch ya, > > Dr. Dallas Warren > Department of Pharmaceutical Biology and Pharmacology > Pharmacy and Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > >> -Original Message- >> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >> Sent: Thursday, 30 April 2009 9:07 AM >> To: jalem...@vt.edu; Discussion list for GROMACS users >> Subject: Re: [gmx-users] Error by pdb2gmx >> >> This is the new entry I added to the rtp file. >> >> [ PDM ] >> >> >> [ atoms ] >> SI SI 0.300 1 >> CH3 opls_069 0.000 1 >> O opls_108 -0.300 1 >> >> >> [ bonds ] >> SI O 0.190 158805.0 >> SI CH3 0.164 293160.0 >> >> >> [ dihedrals ] >> CH3 SI O SI 3.77 3 0 >> SI O SI CH3 3.77 3 0 >> O SI O SI 3.77 3 0 >> >> >> On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul >> wrote: >> > >> > >> > Yanmei Song wrote: >> > >> >> --- >> >> Program pdb2gmx, VERSION 3.3.3 >> >> Source code file: resall.c, line: 289 >> >> >> >> Fatal error: >> >> in .rtp file at line: >> >> >> >> >> >> --- >> > >> > Well that's not a terribly helpful error message, is it? :) >> > >> > There is probably something wrong with the .rtp entry you >> created. If you >> > can post that, perhaps someone can spot it. >> > >> > -Justin >> > >> > -- >> > >> > >> > 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 list gmx-us...@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 >> > >> >> >> >> -- >> Yanmei Song >> Department of Chemical Engineering >>
Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190158805.0 SI CH3 0.164293160.0 [ dihedrals ] CH3SIOSI 3.773 0 SI O SI CH3 3.773 0 OSIOSI 3.773 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> --- >> Program pdb2gmx, VERSION 3.3.3 >> Source code file: resall.c, line: 289 >> >> Fatal error: >> in .rtp file at line: >> >> >> --- > > Well that's not a terribly helpful error message, is it? :) > > There is probably something wrong with the .rtp entry you created. If you > can post that, perhaps someone can spot it. > > -Justin > > -- > > > 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 list gmx-us...@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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Error by pdb2gmx
correct. Fact you can't edit the .rtp file is based on your local > computer system permissions. Normally, best idea is to make your own changes > to a local copy, and use that. > > Catch ya, > > Dr. Dallas Warren > Department of Pharmaceutical Biology and Pharmacology > Pharmacy and Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > >> -Original Message- >> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >> Sent: Wednesday, 29 April 2009 9:24 AM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] Error by pdb2gmx >> >> Dear Dallas: >> >> Thanks for your response. It consists of many repeating units. Do you >> mean I can write the rtp entry for one repeating unit and give it a >> residue name. After that I need to insert this into the force field >> rtp file, right? How can I do that? It seems I can not change the rtp >> file. Thanks. >> >> On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren >> wrote: >> > If it is a repeating unit, then you can build a .rtp entry >> then use it as you would for a protein. >> > >> > Catch ya, >> > >> > Dr. Dallas Warren >> > Department of Pharmaceutical Biology and Pharmacology >> > Pharmacy and Pharmaceutical Sciences, Monash University >> > 381 Royal Parade, Parkville VIC 3010 >> > dallas.war...@pharm.monash.edu.au >> > +61 3 9903 9167 >> > - >> > When the only tool you own is a hammer, every problem >> begins to resemble a nail. >> > >> >> -Original Message- >> >> From: gmx-users-boun...@gromacs.org >> >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >> >> Sent: Wednesday, 29 April 2009 8:59 AM >> >> To: jalem...@vt.edu; Discussion list for GROMACS users >> >> Subject: Re: [gmx-users] Error by pdb2gmx >> >> >> >> Dear Justin: >> >> >> >> Do you have any suggestions on how I can get the itp and >> gro file for >> >> a very long polymer molecules (for example 500 united-atoms), which >> >> only consists of Si, O and C atom. I can use PRODRG to generate a >> >> short chain. But PRODRG has limitation of atom numbers in >> a molecule, >> >> probably less than 300. So any ideas for building up a long chain >> >> based on the short chain? By the way, I already have the >> force field >> >> parameters. >> >> >> >> Thanks a lot! >> >> >> >> On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul >> >> wrote: >> >> > >> >> > >> >> > Yanmei Song wrote: >> >> >> >> >> >> Dear All users: >> >> >> >> >> >> I was trying to set up a long chain polymer system. I got the >> >> >> following PDB file from WebLab. How can I make changes to >> >> the file in >> >> >> order to make it as a GROMACS input pdb file. Then I can >> >> use pdb2gmx >> >> >> to get the gro, itp and top file. >> >> >> >> >> >> When I perform the pdb2gmx command, I got the error message: >> >> >> >> >> >> Residue 'MOL' not found in residue topology database >> >> >> >> >> > >> >> > You can't expect pdb2gmx to be magic. A simple search of >> >> the list archives >> >> > and wiki will turn up the following: >> >> > >> >> > >> >> http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not >> > _found_in_residue_topology_database >> >> > >> >> > -Justin >> >> > >> >> >> Thank you in advance! >> >> >> >> >> >> REMARK Created: Tue Apr 28 15:02:20 US Mountain >> >> Standard Time 2009 >> >> >> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 >> 1.00 0.00 >> >> >> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 >> 1.00 0.00 >> >> >> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 >> 1.00 0.00 >> >> >> ATOM 4 O6 M
Re: [gmx-users] Error by pdb2gmx
Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not change the rtp file. Thanks. On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren wrote: > If it is a repeating unit, then you can build a .rtp entry then use it as you > would for a protein. > > Catch ya, > > Dr. Dallas Warren > Department of Pharmaceutical Biology and Pharmacology > Pharmacy and Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > >> -Original Message- >> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >> Sent: Wednesday, 29 April 2009 8:59 AM >> To: jalem...@vt.edu; Discussion list for GROMACS users >> Subject: Re: [gmx-users] Error by pdb2gmx >> >> Dear Justin: >> >> Do you have any suggestions on how I can get the itp and gro file for >> a very long polymer molecules (for example 500 united-atoms), which >> only consists of Si, O and C atom. I can use PRODRG to generate a >> short chain. But PRODRG has limitation of atom numbers in a molecule, >> probably less than 300. So any ideas for building up a long chain >> based on the short chain? By the way, I already have the force field >> parameters. >> >> Thanks a lot! >> >> On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul >> wrote: >> > >> > >> > Yanmei Song wrote: >> >> >> >> Dear All users: >> >> >> >> I was trying to set up a long chain polymer system. I got the >> >> following PDB file from WebLab. How can I make changes to >> the file in >> >> order to make it as a GROMACS input pdb file. Then I can >> use pdb2gmx >> >> to get the gro, itp and top file. >> >> >> >> When I perform the pdb2gmx command, I got the error message: >> >> >> >> Residue 'MOL' not found in residue topology database >> >> >> > >> > You can't expect pdb2gmx to be magic. A simple search of >> the list archives >> > and wiki will turn up the following: >> > >> > >> http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not > _found_in_residue_topology_database >> > >> > -Justin >> > >> >> Thank you in advance! >> >> >> >> REMARK Created: Tue Apr 28 15:02:20 US Mountain >> Standard Time 2009 >> >> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 >> >> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 >> >> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 >> >> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 >> >> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 >> >> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 >> >> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 >> >> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 >> >> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 >> >> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 >> >> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 >> >> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 >> >> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 >> >> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 >> >> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 >> >> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 >> >> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 >> >> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 >> >> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 >> >> ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 >> >> ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 >> >> ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 >> >> ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 >> >>
Re: [gmx-users] Error by pdb2gmx
Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: >> >> Dear All users: >> >> I was trying to set up a long chain polymer system. I got the >> following PDB file from WebLab. How can I make changes to the file in >> order to make it as a GROMACS input pdb file. Then I can use pdb2gmx >> to get the gro, itp and top file. >> >> When I perform the pdb2gmx command, I got the error message: >> >> Residue 'MOL' not found in residue topology database >> > > You can't expect pdb2gmx to be magic. A simple search of the list archives > and wiki will turn up the following: > > http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database > > -Justin > >> Thank you in advance! >> >> REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 >> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 >> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 >> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 >> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 >> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 >> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 >> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 >> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 >> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 >> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 >> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 >> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 >> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 >> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 >> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 >> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 >> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 >> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 >> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 >> ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 >> ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 >> ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 >> ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 >> ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 >> ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 >> ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 >> ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 >> ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 >> ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 >> ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 >> ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 >> ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 >> ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 >> ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 >> ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 >> ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 >> ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 >> ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 >> ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 >> ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 >> ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00 >> ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00 >> ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 >> ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00 >> ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00 >> TER >> >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar
[gmx-users] Error by pdb2gmx
Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00 ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00 ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00 ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00 TER -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Non-equilibrium Viscosity Calculation
Hi, David; Thank you so much for your prompt response. Your answer is really helpful. On Mon, Apr 20, 2009 at 10:31 PM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Hi, David: >> >> I performed the NEMD and got the following results for averaging the >> last 1 ns. So the second column should be the acceleration and last >> column should be the 1/viscosity. But notice that there are so many >> big negative numbers, which makes the average negative. Can you help >> me out here? what would be possible reason for this. > > xmgrace will tell you which is which, I think the first is shear viscosity > and the second bulk viscosity. Your system might be too smal (Berk Hess > recommends at least 1000 molecules) or the simulation too short. However > bulk viscosity is much more difficult to get right. > Once more, read the literature, and use the tools (xmgrace) the information > is in the xvg file, but you cut it out here. >> >> 1000.61 -0.007012 -369.713501 >> 1020.61 0.006066 320.372314 >> 1040.00 0.002330 122.940369 >> 1060.00 -0.001427 -75.253372 >> 1080.00 0.002888 152.323944 >> 1100.00 0.005696 300.385651 >> 1120.00 0.002224 117.322388 >> 1140.00 0.005990 316.127655 >> 1160.00 0.008966 472.723846 >> 1180.00 0.004485 236.538010 >> 1200.00 -0.000249 -13.136140 >> 1220.00 0.005020 264.962219 >> 1240.00 0.009248 488.308197 >> 1260.00 -0.000559 -29.509850 >> 1280.00 -0.003190 -168.296112 >> 1300.000122 0.002394 126.418747 >> 1320.000122 0.003682 194.374222 >> 1340.000122 0.000371 19.600368 >> 1360.000122 -0.002311 -122.002975 >> 1380.000122 0.001776 93.685326 >> 1400.000122 -0.003357 -177.067062 >> 1420.000122 -0.002963 -156.359772 >> 1440.000122 -0.001078 -56.895496 >> 1460.000122 -0.002273 -119.947853 >> 1480.000122 -0.000658 -34.716648 >> 1500.000122 -0.000928 -48.969398 >> 1520.000122 0.003464 182.804337 >> 1540.000122 -0.001149 -60.652023 >> 1560.000122 0.004629 244.299088 >> 1580.000122 0.000485 25.557356 >> 1600.000122 0.002339 123.374527 >> 1620.000122 0.002612 137.982239 >> 1640.000122 0.002827 149.150589 >> 1660.000122 -0.001614 -85.147079 >> 1680.000122 0.005144 271.660522 >> 1700.000122 -0.002053 -108.302643 >> 1720.000122 0.006096 321.414948 >> 1740.000122 0.006021 317.682129 >> 1760.000122 -0.001203 -63.409481 >> 1780.000122 0.000394 20.755482 >> 1800.000122 0.001910 100.748962 >> 1820.000122 -0.001588 -83.742523 >> 1840.000122 0.002268 119.578842 >> 1860.000122 0.002422 127.769302 >> 1880.000122 -0.000288 -15.188296 >> 1900.000122 0.003324 175.257568 >> 1920.000122 0.003688 194.440231 >> 1940.000122 0.005800 305.705505 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Mon, Apr 20, 2009 at 11:31 AM, David van der Spoel >> wrote: >>> >>> Yanmei Song wrote: >>>> >>>> Yes, I want to get the equilibrium viscosity. My question is how I can >>>> identify the system approach a zero acceleration after I try several >>>> values. Thank you so much for your help. >>> >>> Plot viscosity as a function of acceleration. Check the reference >>> (Wensink >>> et al.) that I mailed earlier. >>>> >>>> On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel >>>> wrote: >>>>> >>>>> Yanmei Song wrote: >>>>>> >>>>>> Dear David: >>>>>> >>>>>> Thank you for your answer. i still have several questions. >>>>>> >>>>>> Do I have to start the non-equilibrium simulation after the system >>>>>> reach the equilibrium? Or I just need to start at the same starting >>>>>> point as the my equilibrium systems? >>>>> >>>>> At least equilibrium density. >>>>>> >>>>>> What I need to do is just add the cos_acceleration: to the mdp file >>>>>> and nothing else need to be changed, right? Also what do you mean by >>>>>> "You need to do a few values such that you can extrapolate to zero >>>>>> accele
Re: [gmx-users] Non-equilibrium Viscosity Calculation
Hi, David: I performed the NEMD and got the following results for averaging the last 1 ns. So the second column should be the acceleration and last column should be the 1/viscosity. But notice that there are so many big negative numbers, which makes the average negative. Can you help me out here? what would be possible reason for this. 1000.61 -0.007012 -369.713501 1020.610.006066 320.372314 1040.000.002330 122.940369 1060.00 -0.001427 -75.253372 1080.000.002888 152.323944 1100.000.005696 300.385651 1120.000.002224 117.322388 1140.000.005990 316.127655 1160.000.008966 472.723846 1180.000.004485 236.538010 1200.00 -0.000249 -13.136140 1220.000.005020 264.962219 1240.000.009248 488.308197 1260.00 -0.000559 -29.509850 1280.00 -0.003190 -168.296112 1300.0001220.002394 126.418747 1320.0001220.003682 194.374222 1340.0001220.000371 19.600368 1360.000122 -0.002311 -122.002975 1380.0001220.001776 93.685326 1400.000122 -0.003357 -177.067062 1420.000122 -0.002963 -156.359772 1440.000122 -0.001078 -56.895496 1460.000122 -0.002273 -119.947853 1480.000122 -0.000658 -34.716648 1500.000122 -0.000928 -48.969398 1520.0001220.003464 182.804337 1540.000122 -0.001149 -60.652023 1560.0001220.004629 244.299088 1580.0001220.000485 25.557356 1600.0001220.002339 123.374527 1620.0001220.002612 137.982239 1640.0001220.002827 149.150589 1660.000122 -0.001614 -85.147079 1680.0001220.005144 271.660522 1700.000122 -0.002053 -108.302643 1720.0001220.006096 321.414948 1740.0001220.006021 317.682129 1760.000122 -0.001203 -63.409481 1780.0001220.000394 20.755482 1800.0001220.001910 100.748962 1820.000122 -0.001588 -83.742523 1840.0001220.002268 119.578842 1860.0001220.002422 127.769302 1880.000122 -0.000288 -15.188296 1900.0001220.003324 175.257568 1920.0001220.003688 194.440231 1940.0001220.005800 305.705505 On Mon, Apr 20, 2009 at 11:31 AM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Yes, I want to get the equilibrium viscosity. My question is how I can >> identify the system approach a zero acceleration after I try several >> values. Thank you so much for your help. > > Plot viscosity as a function of acceleration. Check the reference (Wensink > et al.) that I mailed earlier. >> >> On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel >> wrote: >>> >>> Yanmei Song wrote: >>>> >>>> Dear David: >>>> >>>> Thank you for your answer. i still have several questions. >>>> >>>> Do I have to start the non-equilibrium simulation after the system >>>> reach the equilibrium? Or I just need to start at the same starting >>>> point as the my equilibrium systems? >>> >>> At least equilibrium density. >>>> >>>> What I need to do is just add the cos_acceleration: to the mdp file >>>> and nothing else need to be changed, right? Also what do you mean by >>>> "You need to do a few values such that you can extrapolate to zero >>>> acceleration." >>> >>> You are interested (I assume) in the equilibrium viscosity, therefore you >>> need to do this extrapolation. You can not assume that a small >>> acceleration >>> is small enough. >>>> >>>> After I finish the run, what option I should use for g_energy in order >>>> to get the viscosity? >>> >>> No option. >>> >>> Just do it (tm). >>>> >>>> Thank you so much in advance! >>>> >>>> On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel >>>> wrote: >>>>> >>>>> Yanmei Song wrote: >>>>>> >>>>>> Dear All: >>>>>> >>>>>> I wanted to get the viscosity of my simulated polymer system. From the >>>>>> manual it said that : GROMACS also has a non-equilibrium method for >>>>>> determining the viscosity" (page 123) Does this mean I just need to do >>>>>> a separate non-equilibrium MD run? In terms of mdp file, I just need >>>>>> to add the following options, right? >>>>>> acc_grps: >>>>>> accelerate: >>>>>> cos_acceleration: >>>>> >>>>> Just the last one. >>>>> >>>>>> My question is: first, how to
Re: [gmx-users] Non-equilibrium Viscosity Calculation
Yes, I want to get the equilibrium viscosity. My question is how I can identify the system approach a zero acceleration after I try several values. Thank you so much for your help. On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Dear David: >> >> Thank you for your answer. i still have several questions. >> >> Do I have to start the non-equilibrium simulation after the system >> reach the equilibrium? Or I just need to start at the same starting >> point as the my equilibrium systems? > > At least equilibrium density. >> >> What I need to do is just add the cos_acceleration: to the mdp file >> and nothing else need to be changed, right? Also what do you mean by >> "You need to do a few values such that you can extrapolate to zero >> acceleration." > > You are interested (I assume) in the equilibrium viscosity, therefore you > need to do this extrapolation. You can not assume that a small acceleration > is small enough. >> >> After I finish the run, what option I should use for g_energy in order >> to get the viscosity? > > No option. > > Just do it (tm). >> >> Thank you so much in advance! >> >> On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel >> wrote: >>> >>> Yanmei Song wrote: >>>> >>>> Dear All: >>>> >>>> I wanted to get the viscosity of my simulated polymer system. From the >>>> manual it said that : GROMACS also has a non-equilibrium method for >>>> determining the viscosity" (page 123) Does this mean I just need to do >>>> a separate non-equilibrium MD run? In terms of mdp file, I just need >>>> to add the following options, right? >>>> acc_grps: >>>> accelerate: >>>> cos_acceleration: >>> >>> Just the last one. >>> >>>> My question is: first, how to set the value of cos_acceleration: ? >>> >>> You need to do a few values such that you can extrapolate to zero >>> acceleration. >>> >>>> Second, after I finish the run, how can I get the viscosity from the >>>> simulation result? Anyone has done this yet? Thank you so much for >>>> your answer in advance. >>>> >>> g_energy. >>> >>> J Chem Phys 116 (2002) 209-217 >>> J Chem Phys 119 (2003) 7308-7317 >>>> >>> >>> -- >>> 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.se sp...@gromacs.org http://folding.bmc.uu.se >>> ___ >>> gmx-users mailing list gmx-us...@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.se sp...@gromacs.org http://folding.bmc.uu.se > ___ > gmx-users mailing list gmx-us...@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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Non-equilibrium Viscosity Calculation
Dear David: Thank you for your answer. i still have several questions. Do I have to start the non-equilibrium simulation after the system reach the equilibrium? Or I just need to start at the same starting point as the my equilibrium systems? What I need to do is just add the cos_acceleration: to the mdp file and nothing else need to be changed, right? Also what do you mean by "You need to do a few values such that you can extrapolate to zero acceleration." After I finish the run, what option I should use for g_energy in order to get the viscosity? Thank you so much in advance! On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Dear All: >> >> I wanted to get the viscosity of my simulated polymer system. From the >> manual it said that : GROMACS also has a non-equilibrium method for >> determining the viscosity" (page 123) Does this mean I just need to do >> a separate non-equilibrium MD run? In terms of mdp file, I just need >> to add the following options, right? >> acc_grps: >> accelerate: >> cos_acceleration: > > Just the last one. > >> >> My question is: first, how to set the value of cos_acceleration: ? > > You need to do a few values such that you can extrapolate to zero > acceleration. > >> Second, after I finish the run, how can I get the viscosity from the >> simulation result? Anyone has done this yet? Thank you so much for >> your answer in advance. >> > g_energy. > > J Chem Phys 116 (2002) 209-217 > J Chem Phys 119 (2003) 7308-7317 >> >> > > > -- > 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.se sp...@gromacs.org http://folding.bmc.uu.se > ___ > gmx-users mailing list gmx-us...@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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] g_msd
I had the same problem before. I think the best way to do it is to analyze every group separately. On Mon, Apr 20, 2009 at 1:53 AM, Borys Szefczyk wrote: > Dear Gromacs users, > > I'm doing some tests on molten sodium chloride, trying to calculate > self-diffusion coefficients of both ions. Could someone tell me what > actually does the -ngroup switch of the g_msd program? > > When I compute D for chlorine only, I get 6.4607e-5 cm^2/s; > for sodium only, I get D = 9.0996e-5 cm^2/s. > > But when I set -ngroup to 2 and specify both groups (NA and CL) > subsequently, I get: > D[ NA+] = 9.0976e-5 cm^2/s > D[ CL-] = 0.9128e-5 cm^2/s > Plot of MSD looks fine for NA, but not for CL - it's a saw-shaped, > almost flat line. > > If I enter the groups in reverse order, first CL, then NA, I get: > D[ CL-] = 6.4607e-5 cm^2/s > D[ NA+] = 4.2326e-5 cm^2/s > Again, first plot look fine, the second - not. > > Why these results differ? > > Regards, > Borys Szefczyk > > > -- > REQUIMTE, & Molecular Modelling & Quantum Chemistry Group, > Department of Chemistry, & Institute of Physical & Theoretical Chemistry, > Faculty of Science, & Wroclaw University of Technology > University of Porto & http://ichfit.ch.pwr.wroc.pl/people/szefczyk > ___ > gmx-users mailing list gmx-us...@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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Non-equilibrium Viscosity Calculation
Dear All: I wanted to get the viscosity of my simulated polymer system. From the manual it said that : GROMACS also has a non-equilibrium method for determining the viscosity" (page 123) Does this mean I just need to do a separate non-equilibrium MD run? In terms of mdp file, I just need to add the following options, right? acc_grps: accelerate: cos_acceleration: My question is: first, how to set the value of cos_acceleration: ? Second, after I finish the run, how can I get the viscosity from the simulation result? Anyone has done this yet? Thank you so much for your answer in advance. -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to calculate the viscosity of the bulk
Hi, Berk: I saw your paper about the viscosity calculation method. Can you tell me what exactly I should do using GROMACS to get the fluid viscosity? I used GROMACS-3.3.3 single precision. Thanks a lot in advance. On Tue, Feb 3, 2009 at 1:58 AM, Berk Hess wrote: > Hi, > > This Einstein method of g_energy is extremely sensitive to the system setup. > You should have perfect pressure fluctuations, which probably means shifted > LJ potential, > PME, constant volume and double precision. > Some time ago I made a comparison of different methods: > http://dx.doi.org/10.1063/1.1421362 > Two of the methods can be used via the mdp option cos_acceleration and the > tool g_tcaf. > > David, I think we should remove the -vis option of g_energy, > since it will give nonsens, unless you know exactly what you are doing. > In that case you can also evaluate the Einstein formula "by hand" from the > pressure. > > Berk > >> Date: Mon, 2 Feb 2009 19:34:59 -0500 >> From: jalem...@vt.edu >> To: gmx-users@gromacs.org >> Subject: Re: [gmx-users] how to calculate the viscosity of the bulk >> >> >> >> Yanmei Song wrote: >> > Hi, Justin: >> > >> > I saw in the manual that by g_energy -vis the viscosity of the system >> > can be calculated. But when I perform the command i got this: >> > >> > @ title "Bulk Viscosity" >> > @ xaxis label "Time (ps)" >> > @ yaxis label "\8h\4 (cp)" >> > @TYPE xy >> > @ view 0.15, 0.15, 0.75, 0.85 >> > @ legend on >> > @ legend box on >> > @ legend loctype view >> > @ legend 0.78, 0.8 >> > @ legend length 2 >> > @ s0 legend "Shear" >> > @ s1 legend "Bulk" >> > 19.9601 182.954 131.299 >> > 39.9202 195.973 134.808 >> > 59.8802 209.345 130.015 >> > 79.8403 220.959 129.291 >> > 99.8004 227.397 133.514 >> > 119.76 224.858 128.183 >> > 139.721 234.26 124.201 >> > 159.681 239.432 112.779 >> > 179.641 233.247 90.5362 >> > 199.601 235.796 83.3315 >> > 219.561 232.205 80.3525 >> > 239.521 219.87 78.862 >> > 259.481 216.261 84.9063 >> > 279.441 221.782 81.2453 >> > 299.401 221.704 76.6335 >> > 319.361 212.225 83.4834 >> > 339.321 209.746 95.7125 >> > 359.281 208.776 100.049 >> > 379.242 209.623 101.467 >> > 399.202 204.93 111.357 >> > 419.162 196.223 117.499 >> > 439.122 198.347 121.818 >> > 459.082 200.15 118.537 >> > 479.042 203.718 105.464 >> > 499.002 209.584 98.6823 >> > 518.962 215.025 101.854 >> > 538.922 226.533 102.949 >> > 558.882 229.609 97.6396 >> > 578.842 228.081 96.0029 >> > 598.802 237.529 95.4091 >> > 618.762 245.169 95.4332 >> > 638.723 253.263 97.1168 >> > 658.683 251.794 86.5936 >> > 678.643 242.619 72.306 >> > 698.603 235.621 63.5751 >> > 718.563 230.813 67.5429 >> > 738.523 236.095 78.8719 >> > 758.483 240.001 84.0771 >> > 778.443 246.356 88.0818 >> > 798.403 256.28 91.1965 >> > 818.363 267.644 95.403 >> > 838.323 272.758 102.16 >> > 858.283 278.369 101.837 >> > 878.243 281.149 98.535 >> > 898.204 268.186 93.7993 >> > 918.164 254.442 81.3065 >> > 938.124 239.547 78.0454 >> > 958.084 221.896 87.4938 >> > 978.044 213.811 103.699 >> > 998.004 207.287 113.678 >> > >> > >> > My question is what the value should be for the viscosity of the >> > fluid. Should I average all the values of third column to get the >> > value. Does the value have a unit of cp? >> > >> >> Don't know, I've never done viscosity measurements before. Luckily, the >> Gromacs >> output is quite informative. Have you opened this file in xmgrace? It will >> make life a lot easier to read the graph. Units and legends are provided >> to >> indicate what the data mean. >> >> -Justin >> >> > Thank you so much in advance! >> > >> > Yanmei Song >> > Department of Chemical Engineering >> > ASU >> > ___ >> > 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! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gr
Re: [gmx-users] how to calculate the viscosity of the bulk
Dear All: Does anyone knows how to calculate the viscosity of the simulated system except the g_energy -vis. Because I saw some literature that they can get the viscosity but I don't know how.Thanks a lot! On Tue, Feb 3, 2009 at 1:58 AM, Berk Hess wrote: > Hi, > > This Einstein method of g_energy is extremely sensitive to the system setup. > You should have perfect pressure fluctuations, which probably means shifted > LJ potential, > PME, constant volume and double precision. > Some time ago I made a comparison of different methods: > http://dx.doi.org/10.1063/1.1421362 > Two of the methods can be used via the mdp option cos_acceleration and the > tool g_tcaf. > > David, I think we should remove the -vis option of g_energy, > since it will give nonsens, unless you know exactly what you are doing. > In that case you can also evaluate the Einstein formula "by hand" from the > pressure. > > Berk > >> Date: Mon, 2 Feb 2009 19:34:59 -0500 >> From: jalem...@vt.edu >> To: gmx-users@gromacs.org >> Subject: Re: [gmx-users] how to calculate the viscosity of the bulk >> >> >> >> Yanmei Song wrote: >> > Hi, Justin: >> > >> > I saw in the manual that by g_energy -vis the viscosity of the system >> > can be calculated. But when I perform the command i got this: >> > >> > @ title "Bulk Viscosity" >> > @ xaxis label "Time (ps)" >> > @ yaxis label "\8h\4 (cp)" >> > @TYPE xy >> > @ view 0.15, 0.15, 0.75, 0.85 >> > @ legend on >> > @ legend box on >> > @ legend loctype view >> > @ legend 0.78, 0.8 >> > @ legend length 2 >> > @ s0 legend "Shear" >> > @ s1 legend "Bulk" >> > 19.9601 182.954 131.299 >> > 39.9202 195.973 134.808 >> > 59.8802 209.345 130.015 >> > 79.8403 220.959 129.291 >> > 99.8004 227.397 133.514 >> > 119.76 224.858 128.183 >> > 139.721 234.26 124.201 >> > 159.681 239.432 112.779 >> > 179.641 233.247 90.5362 >> > 199.601 235.796 83.3315 >> > 219.561 232.205 80.3525 >> > 239.521 219.87 78.862 >> > 259.481 216.261 84.9063 >> > 279.441 221.782 81.2453 >> > 299.401 221.704 76.6335 >> > 319.361 212.225 83.4834 >> > 339.321 209.746 95.7125 >> > 359.281 208.776 100.049 >> > 379.242 209.623 101.467 >> > 399.202 204.93 111.357 >> > 419.162 196.223 117.499 >> > 439.122 198.347 121.818 >> > 459.082 200.15 118.537 >> > 479.042 203.718 105.464 >> > 499.002 209.584 98.6823 >> > 518.962 215.025 101.854 >> > 538.922 226.533 102.949 >> > 558.882 229.609 97.6396 >> > 578.842 228.081 96.0029 >> > 598.802 237.529 95.4091 >> > 618.762 245.169 95.4332 >> > 638.723 253.263 97.1168 >> > 658.683 251.794 86.5936 >> > 678.643 242.619 72.306 >> > 698.603 235.621 63.5751 >> > 718.563 230.813 67.5429 >> > 738.523 236.095 78.8719 >> > 758.483 240.001 84.0771 >> > 778.443 246.356 88.0818 >> > 798.403 256.28 91.1965 >> > 818.363 267.644 95.403 >> > 838.323 272.758 102.16 >> > 858.283 278.369 101.837 >> > 878.243 281.149 98.535 >> > 898.204 268.186 93.7993 >> > 918.164 254.442 81.3065 >> > 938.124 239.547 78.0454 >> > 958.084 221.896 87.4938 >> > 978.044 213.811 103.699 >> > 998.004 207.287 113.678 >> > >> > >> > My question is what the value should be for the viscosity of the >> > fluid. Should I average all the values of third column to get the >> > value. Does the value have a unit of cp? >> > >> >> Don't know, I've never done viscosity measurements before. Luckily, the >> Gromacs >> output is quite informative. Have you opened this file in xmgrace? It will >> make life a lot easier to read the graph. Units and legends are provided >> to >> indicate what the data mean. >> >> -Justin >> >> > Thank you so much in advance! >> > >> > Yanmei Song >> > Department of Chemical Engineering >> > ASU >> > ___ >> > 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! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@grom
[gmx-users] how to calculate the viscosity of the bulk
Hi, Justin: I saw in the manual that by g_energy -vis the viscosity of the system can be calculated. But when I perform the command i got this: @title "Bulk Viscosity" @xaxis label "Time (ps)" @yaxis label "\8h\4 (cp)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Shear" @ s1 legend "Bulk" 19.9601 182.954 131.299 39.9202 195.973 134.808 59.8802 209.345 130.015 79.8403 220.959 129.291 99.8004 227.397 133.514 119.76 224.858 128.183 139.721 234.26 124.201 159.681 239.432 112.779 179.641 233.247 90.5362 199.601 235.796 83.3315 219.561 232.205 80.3525 239.521 219.87 78.862 259.481 216.261 84.9063 279.441 221.782 81.2453 299.401 221.704 76.6335 319.361 212.225 83.4834 339.321 209.746 95.7125 359.281 208.776 100.049 379.242 209.623 101.467 399.202 204.93 111.357 419.162 196.223 117.499 439.122 198.347 121.818 459.082 200.15 118.537 479.042 203.718 105.464 499.002 209.584 98.6823 518.962 215.025 101.854 538.922 226.533 102.949 558.882 229.609 97.6396 578.842 228.081 96.0029 598.802 237.529 95.4091 618.762 245.169 95.4332 638.723 253.263 97.1168 658.683 251.794 86.5936 678.643 242.619 72.306 698.603 235.621 63.5751 718.563 230.813 67.5429 738.523 236.095 78.8719 758.483 240.001 84.0771 778.443 246.356 88.0818 798.403 256.28 91.1965 818.363 267.644 95.403 838.323 272.758 102.16 858.283 278.369 101.837 878.243 281.149 98.535 898.204 268.186 93.7993 918.164 254.442 81.3065 938.124 239.547 78.0454 958.084 221.896 87.4938 978.044 213.811 103.699 998.004 207.287 113.678 My question is what the value should be for the viscosity of the fluid. Should I average all the values of third column to get the value. Does the value have a unit of cp? Thank you so much in advance! Yanmei Song Department of Chemical Engineering ASU ___ 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] Question about the pairs parameters
Hi, If I want to define non bonded interactions in my top. I already have the sigma and epsi values. What I wanted to do is to to use combination rule 2, then how should I write the pairs part? ai aj fuc0, c1, ... 1 6 1 ; CAA CBH 2 7 1 ; CBF CAG 2 8 1 ; CBF CAH 2 9 1 ; CBF OAY 3 6 1 ; CAB CBH 4 6 1 ; CAC CBH 5 10 1 ; OAW CBJ So does the function here means the combination rule, or I need to define it in [defaults] ? if it is the latter, then what does the functions means here? The value i need to put here for c0 and c1 then should be sigma and epsi, right? Thank you so much for your answer in advance! -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Question about the dihedrals in top file using OPLS force field in GROMACS
[ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 1 2 5 6 10.03.77 30.03.77 3 ; dih CAA CBF OAW CBH 2 5 6 9 10.03.77 30.03.77 3 ; dih CBF OAW CBH OAY 5 6 9 10 10.03.77 30.03.77 3 ; dih OAW CBH OAY CBJ 6 9 10 13 10.03.77 30.03.77 3 ; dih CBH OAY CBJ OBA 9 10 13 14 10.03.77 30.03.77 3 ; dih OAY CBJ OBA CBL Sorry to bother you so much times. Above is the real parameter I used in my top file which probably specified the dihedrals as periodic (function 1) . But I also used OPLS force field which should read different parameters as RB. So when the MD runs, does it just read this parameters in the periodic dihedrals as a RB parameter? If my top is in a wrong form, how can md runs well and give a good result? 2009/1/28 Justin A. Lemkul : > > > Yanmei Song wrote: >> >> What makes me so confused is that I used this top for the MD run using >> ffoplsaa.itp and the there are no error message. Also I got a good >> result compared to experiment. Does it mean that what I did is totally >> wrong with using this top in combination with OPLS? >> > > Well, the numbers in the .top for the dihedrals were designed to be > components of a periodic dihedral (function type 1 in the .top), which is > not of the same form as an R-B dihedral (function type 3). My guess would > be that the parameters you have specified are not appropriate for use with > OPLS. > >> Also if I used the atom type in opls_x with the x is less than 135, >> then it should be OPLS UA force field right? if I want to use OPLS, >> How can we get the top? Thank you so much for your help! >> > > I suppose you would have OPLS UA, as far as your atom types are concerned. > I don't know for sure, I've never used the UA version of OPLS. If you want > the .top for your own molecule, you may have to write it by hand, perhaps > even using the PRODRG topology as a skeleton (along with a thorough > understanding of Chapter 5 of the manual, as Mark advised). Depending on > the size of your molecule, this manual process may be a chore, so you could > also consider making an entry for your molecule within ffoplsaa.rtp. Make > a local copy in the working directory to ensure that you don't break > something by accident! > > -Justin > >> 2009/1/28 Justin A. Lemkul : >>> >>> Yanmei Song wrote: >>>> >>>> Hi,Justin: >>>> >>>> Thanks for your response. >>>> >>>> I have read that part and still confused. Does it mean that if I >>>> choose the ffoplsaa.itp in my top, I used the RB potential for >>>> Dihedrals or the periodic type? Also actually I can only get the >>>> parameters for phi, cp and mult (listed above) Can I use these >>>> parameters directly for my itp user ffoplsaa force field? Thanks a >>>> lot! >>>> >>> OPLS does use the R-B potential. It looks like that topology is a PRODRG >>> product, in which case, no, your topology is not suitable for use with >>> OPLS. >>> PRODRG generates Gromos-type topologies. >>> >>> -Justin >>> >>>> 2009/1/28 Justin A. Lemkul : >>>>> >>>>> Yanmei Song wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> I am using ffoplsaa.itp as my force field to do a simulation using >>>>>> GROMACS. >>>>>> I have a question about how to write the parameters in dihedrals in >>>>>> the itp file. >>>>>> >>>>>> [ dihedrals ] >>>>>> ; ai aj ak al fuc0, c1, m, ... >>>>>> 1 2 5 6 10.03.77 30.03.77 3 ; dih CAA >>>>>> CBF OAW CBH >>>>>> 2 5 6 9 10.03.77 30.03.77 3 ; dih CBF >>>>>> OAW CBH OAY >>>>>> 5 6 9 10 10.03.77 30.03.77 3 ; dih OAW >>>>>> CBH OAY CBJ >>>>>> 6 9 10 13 10.03.77 30.03.77 3 ; dih CBH >>>>>> OAY CBJ OBA >>>>>> 9 10 13 14 10.03.77 30.03.77 3 ; dih OAY >>>>>> CBJ OBA CBL >>>>>> >>>>>> Then if I am choosing ffoplsaa.itp force field, what is the meaning >>>>>> for c0,c1 and m under the [dihedrals]? Since i know that GROMOS and >>>>>> OPLS force field have a different format for prope
Re: [gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS
What makes me so confused is that I used this top for the MD run using ffoplsaa.itp and the there are no error message. Also I got a good result compared to experiment. Does it mean that what I did is totally wrong with using this top in combination with OPLS? Also if I used the atom type in opls_x with the x is less than 135, then it should be OPLS UA force field right? if I want to use OPLS, How can we get the top? Thank you so much for your help! 2009/1/28 Justin A. Lemkul : > > > Yanmei Song wrote: >> >> Hi,Justin: >> >> Thanks for your response. >> >> I have read that part and still confused. Does it mean that if I >> choose the ffoplsaa.itp in my top, I used the RB potential for >> Dihedrals or the periodic type? Also actually I can only get the >> parameters for phi, cp and mult (listed above) Can I use these >> parameters directly for my itp user ffoplsaa force field? Thanks a >> lot! >> > > OPLS does use the R-B potential. It looks like that topology is a PRODRG > product, in which case, no, your topology is not suitable for use with OPLS. > PRODRG generates Gromos-type topologies. > > -Justin > >> 2009/1/28 Justin A. Lemkul : >>> >>> Yanmei Song wrote: >>>> >>>> Hi, >>>> >>>> I am using ffoplsaa.itp as my force field to do a simulation using >>>> GROMACS. >>>> I have a question about how to write the parameters in dihedrals in >>>> the itp file. >>>> >>>> [ dihedrals ] >>>> ; ai aj ak al fuc0, c1, m, ... >>>> 1 2 5 6 10.03.77 30.03.77 3 ; dih CAA >>>> CBF OAW CBH >>>> 2 5 6 9 10.03.77 30.03.77 3 ; dih CBF >>>> OAW CBH OAY >>>> 5 6 9 10 10.03.77 30.03.77 3 ; dih OAW >>>> CBH OAY CBJ >>>> 6 9 10 13 10.03.77 30.03.77 3 ; dih CBH >>>> OAY CBJ OBA >>>> 9 10 13 14 10.03.77 30.03.77 3 ; dih OAY >>>> CBJ OBA CBL >>>> >>>> Then if I am choosing ffoplsaa.itp force field, what is the meaning >>>> for c0,c1 and m under the [dihedrals]? Since i know that GROMOS and >>>> OPLS force field have a different format for proper dihedrals. For >>>> OPLS it seems there are four other parameter like v1 v2 v3 v4. Then my >>>> question is how can i define the dihedral parameters in itp file based >>>> on ffoplsaa force field in GROMACS? Thanks a lot! >>>> >>> Refer to the manual, section 4.2.12 "Proper Dihedrals." >>> >>> -Justin >>> >>>> Yanmei >>> >>> -- >>> >>> >>> Justin A. Lemkul >>> Graduate Research Assistant >>> 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://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 >>> >> >> >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > 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://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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Question about the dihedrals in top file using OPLS force field in GROMACS
Hi,Justin: Thanks for your response. I have read that part and still confused. Does it mean that if I choose the ffoplsaa.itp in my top, I used the RB potential for Dihedrals or the periodic type? Also actually I can only get the parameters for phi, cp and mult (listed above) Can I use these parameters directly for my itp user ffoplsaa force field? Thanks a lot! 2009/1/28 Justin A. Lemkul : > > > Yanmei Song wrote: >> >> Hi, >> >> I am using ffoplsaa.itp as my force field to do a simulation using >> GROMACS. >> I have a question about how to write the parameters in dihedrals in >> the itp file. >> >> [ dihedrals ] >> ; ai aj ak al fuc0, c1, m, ... >> 1 2 5 6 10.03.77 30.03.77 3 ; dih CAA >> CBF OAW CBH >> 2 5 6 9 10.03.77 30.03.77 3 ; dih CBF >> OAW CBH OAY >> 5 6 9 10 10.03.77 30.03.77 3 ; dih OAW >> CBH OAY CBJ >> 6 9 10 13 10.03.77 30.03.77 3 ; dih CBH >> OAY CBJ OBA >> 9 10 13 14 10.03.77 30.03.77 3 ; dih OAY >> CBJ OBA CBL >> >> Then if I am choosing ffoplsaa.itp force field, what is the meaning >> for c0,c1 and m under the [dihedrals]? Since i know that GROMOS and >> OPLS force field have a different format for proper dihedrals. For >> OPLS it seems there are four other parameter like v1 v2 v3 v4. Then my >> question is how can i define the dihedral parameters in itp file based >> on ffoplsaa force field in GROMACS? Thanks a lot! >> > > Refer to the manual, section 4.2.12 "Proper Dihedrals." > > -Justin > >> Yanmei > > -- > > > Justin A. Lemkul > Graduate Research Assistant > 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://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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Question about the dihedrals in top file using OPLS force field in GROMACS
Hi, I am using ffoplsaa.itp as my force field to do a simulation using GROMACS. I have a question about how to write the parameters in dihedrals in the itp file. [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 1 2 5 6 10.03.77 30.03.77 3 ; dih CAA CBF OAW CBH 2 5 6 9 10.03.77 30.03.77 3 ; dih CBF OAW CBH OAY 5 6 9 10 10.03.77 30.03.77 3 ; dih OAW CBH OAY CBJ 6 9 10 13 10.03.77 30.03.77 3 ; dih CBH OAY CBJ OBA 9 10 13 14 10.03.77 30.03.77 3 ; dih OAY CBJ OBA CBL Then if I am choosing ffoplsaa.itp force field, what is the meaning for c0,c1 and m under the [dihedrals]? Since i know that GROMOS and OPLS force field have a different format for proper dihedrals. For OPLS it seems there are four other parameter like v1 v2 v3 v4. Then my question is how can i define the dihedral parameters in itp file based on ffoplsaa force field in GROMACS? Thanks a lot! Yanmei -- Yanmei Song Department of Chemical Engineering ASU ___ 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
