[gmx-users] gmx-users@gromacs.org
Finally had a look through the gromacs 4.0 source code. Don't know if this bug/points already have been reported and changed in 4.0.2: 1) There is never memory allocated for the pointers to the user defined groups: mdatoms->cU1 etc. These pointers will stay NULL when a user defined group is defined in the mdp file. I find these groups normally a pretty useful interface for simple fast implementations. 2) The pull code has indeed completely changed, however to me the questionable factor 0.5 remained the same: In pull.c: /* Add the pull contribution to the virial */ vir[j][m] += 0.5*f[j]*r_ij[g][m]; I do agree with the positive sign of the summation, but why is there a factor 0.5 to correct for double counting included in the summation. The summation is already ordered as r_ij and f[j] is the distance vector and force between the particle and the equilibrium position of the spring and therefore double counting cannot occur. Ofcourse it's possible that this factor 0.5 is not meant as a double counting correction factor, but then I don't see where it does come from. If this factor is indeed incorrect it might affect the pressure significantly in case a large pulling group is used. greetings Jelger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: abnormal flip-flop when embedding cholesterol into DOPC using CG
Dear Ran, Indeed, strictly speaking a smaller time step will give you a more precise intergration over phase-space. However, as the CG-model itself and theirfore its corresponding energy description are parametrized for only a certain range in time steps. The extra details which one gains with a more precise intergration over the energy field by chosing a much smaller time step are beyond the actual "resolution" of the CG-model and therefore not physical. .About the flip-flop problem. Please be more precize. Describe what is a high rate in flip-flops and how long you have simulated. The change of DOPC in cholesterol will give a dramatic change in the area per lipid. What one sees is probably a system trying to equlibrate itself. Does the problem still continue, after lets say 50 ns ? Good luck, greetings JElger On Thu, 06 Dec 2007 10:17:42 +0100 Ran Friedman <[EMAIL PROTECTED]> wrote: Dear Xavier, GMX users, Xavier Periole wrote: One other thing. In the CG FF the time step is considered as part of the force field. Meaning that you should not play with it too much. 0.04-0.02 ps is the actual range where the force field is considered to reproduce experimental values of various quantities used for paraameterization of the FF. Outside this range you change the balance between the different terms and thus would alter the quality of the FF. Can you elaborate on this a bit? Surely if one changes the temperature, pressure, compressibility, threshold distances etc., one doesn't necessarily reproduces the experimental results. Too long timesteps may also cause a problem. But why would it be wrong to use a shorter time step here? Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] on NVE and pressure
On Mon, 16 Apr 2007 09:40:58 +0200 lorix <[EMAIL PROTECTED]> wrote: Hi everybody, I am simulating a protein (approximately 5000 atoms) in water (35000 atoms). The protein is out of a thermodynamic equilibrium because I modified a crystallographic structure of one of its conformation (which showed stability with MD). Thus, my aim would be to let the system evolve to a new equilibrium. I am expecting a conformation for the protein smaller in size than the starting point. I had several simulations with Temperature and pressure coupling and now I have decided to go for NVE (after a prior equilibration with TP controls for 300 K and 1 bar) , the decision is mainly because I do not want to affect the evolution of atom velocities during the simulation. With the NVE ensemble after 2 nsec I have an average value for Temperature about 285 K while the Pressure average value is around -230 bar. The temperature is clearly fine. While the big negative value for pressure is meaning that the system wants to contract if I understood correctly ? How does this pressure affect the system? Have I to consider the pressure just like a tendency of the system either to contract or to expand? thanks for any suggestion loris... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hi Lorix, Don't worry ;-) Because actually there is no thermodynamic sense of defining pressure in a NVE ensemble at all. In the thermodynamic limit pressure is defined as: -(dE/dV)=p, while in the microcanonical ensemble E,V are constant. The definition of pressure in Gromacs arises from mathematically constructed stresses on a nanoscopic system. So when doing NVE, you still get your numbers but puristically speaking it doesn't mean much. greetings Jelger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] hessian_matrix_from_ordered_trajectory
On Thu, 5 Apr 2007 18:53:58 +0200 Sang-Min Park <[EMAIL PROTECTED]> wrote: Dear all, I calculated the eigenvalues and eigenvectors from a small peptide with a closest water neighboorhood watersurrounding. To do this I generated a new trajectory with the command "trjorder" to order the watermolecules in a way so that they are close to the center of mass of the peptide. From this new trajectory I took only the subsystem "Peptide+ the first 20 closest water" and generated the Hessian. When I look at the input-files,needed to generate the matrix I see that one need only the configuration, a top file and a mdp file. (for grompp). So this would mean, that gromacs would calculate the Potential (the second derivate of the potential) from this configuration and then calculate the hessian matrix. Furthermore I calculated the Hessian at every snapshot of the trajectory. I tested if its work right and calculated the hessian matrix from the same configuration, but only changed 2 watermolecules in their index i. (see the tables below) for example: old configuation new configuration i coordinates i coord. 12 O xO1 yO1 zO1 12 O xO2 yO2 zO2 12 H xH11 yH11 zH11(change index)12 H xH21 yH21 zH21 12 H xH12 yH12 zH12--> 12 H xH22 y22 zH22 ... ... ... ... 22 O xO2 yO2 zO2 22 O xO1 yO1 zO1 22 H xH21 yH21 zH21 22 H xH11 yH11 zH11 22 H xH22 yH22 zH22 22 H xH12 yH12 zH12 ... ... ... ... In most cases I got the same eigenvalues and eigenvectors but in some cases the results were very different. What could be the reason? Thank you in advance Sang Min ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php I'm not sure if I understand you correctly : You generated a configuration file of the 20 nearest water molecules. That means that the index and identity of the 20 waters can differ in each snapshot, however in the top file 20 is 20 and names neither numbers don't matter. So the actual identity should not play a role in for the production of tpr. No you switch the order of lets say: water molecule 19 with 20. When you do this you find different eigenvalues of the hessian in some casescorrect ? The dimension of the hessian is Nx3,Nx3, in which you have i=1,2Nx3 rows and collums. Each element i has the same order as in the gro file (1,2N). So if you switch a line in the gro the hessian is different too. Although the hessian will allways be build up from the same set of numbers...it will simply not be the same matrix (permutations). So actually I don't really think this way is a good way to study the time evolution of the hessian. Better just take the protein, peptide or wathever without the water. Did you check if the trace of the hessian (sum of all eigen values) is more close to constant ? Anyway, Good luck. greetings Jelger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Can I run BD in water media using Gmx? (H.J.Risselada)
On Thu, 11 Jan 2007 09:50:12 +0800 "Hu Zhongqiao" <[EMAIL PROTECTED]> wrote: Thanks, Mark and Jelger, To Jelger, But If one can run BD by setting integrator=sd, how is dielectri constant of water set in the simulation? On p141 of the Manual v3.3, there is one option epsilon_r. Does it mean BD can be run successfully if epsilon_r is set as ca. 78 for water? zhongqiao GROMACS does not permit implicit solvent models for any of its integration methods. Other simulation packages do. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php If I am not mistaken implicit solvent is implemented in GMX for using sd integration. (Never did any proteins ;), so don't blame me if I'm wrong.) The GB82 langevin integrator implemented in gromacs (option "sd" in mdp file) is however a generalized langevin integrator. The BD euler scheme (bd in mdp file), is just a solution of the same differential equation as the SD equation, however now this differential equation can be simplified as some terms (inertia) become insignificant in the limit of high friction. "Generalized" means that the sd-scheme in gromacs is capable to solve the equations of motions in both the newtonian limit (tau_t >>> 0) as well as in the brownian regime (tau_t -> 0 ). Ofcourse, it can still only handle the friction coefficients in the limits to some numerical extend. If the friction coefficent is reasonable small you will be still able to do brownian dynamics with the sd integrator and use implicit solvent options. Anyway, Good luck !!! greetings Jelger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php For specific questions, my former collegue Fan Hao was doing implicit solvent simulation in gromacs using non-public available code. I initialy thought it allready had been standardized in gromacs.but probably not... (why not ?). I will send you his email adress. gr Jelger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Can I run BD in water media using Gmx? (Hu Zhongqiao)
On Wed, 10 Jan 2007 17:36:10 +1100 Mark Abraham <[EMAIL PROTECTED]> wrote: Hu Zhongqiao wrote: Hi, Nobody implied me till now. So that means the current version can not do BD by implicitly treating water into continuum media, i.e, use of dielectric constant of water. I hope Gmx developers can help me to make sure this. Till to now I am been using Gmx and in the near future I need to do BD for longer time scale. If Gmx can not help, it will be bad. GROMACS does not permit implicit solvent models for any of its integration methods. Other simulation packages do. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php If I am not mistaken implicit solvent is implemented in GMX for using sd integration. (Never did any proteins ;), so don't blame me if I'm wrong.) The GB82 langevin integrator implemented in gromacs (option "sd" in mdp file) is however a generalized langevin integrator. The BD euler scheme (bd in mdp file), is just a solution of the same differential equation as the SD equation, however now this differential equation can be simplified as some terms (inertia) become insignificant in the limit of high friction. "Generalized" means that the sd-scheme in gromacs is capable to solve the equations of motions in both the newtonian limit (tau_t >>> 0) as well as in the brownian regime (tau_t -> 0 ). Ofcourse, it can still only handle the friction coefficients in the limits to some numerical extend. If the friction coefficent is reasonable small you will be still able to do brownian dynamics with the sd integrator and use implicit solvent options. Anyway, Good luck !!! greetings Jelger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
