[gmx-users] Number of Frames in Trajectory
Dear users, Am trying to simulate a polymer in vaccum.But when i make the production run and view trajectory(.trr) files in VMD am getting only one frame.Here's a part of my mdp file: title = polymer cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.005; nsteps = 5; nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps= BEN NCH0 ref_t = 300 300 ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 But the mdrun given for equilibriation step generated 96 frames.Is that because of the algorithm that i specified in the integrtaor as MD.Because other than md,when i gave bd or steep am getting more frames.So what is the problem in obtining frames with md as input for integrator? ___ 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] Number of Frames in Trajectory
varsha gautham wrote: Dear users, Am trying to simulate a polymer in vaccum.But when i make the production run and view trajectory(.trr) files in VMD am getting only one frame.Here's a part of my mdp file: title = polymer cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.005; nsteps = 5; nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 1000 Are you sure you want positions, velocities and forces every thousand steps? What are you going to do with the latter two? Check out the manual, chapter 7. nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps= BEN NCH0 ref_t = 300 300 ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 But the mdrun given for equilibriation step generated 96 frames.Is that Not possible - the above would generate at most 50. because of the algorithm that i specified in the integrtaor as MD.Because other than md,when i gave bd or steep am getting more frames.So what is the problem in obtining frames with md as input for integrator? MD does MD, not energy minimization, as those others do. 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
[gmx-users] how to get a solvent density map using volumeslice in VMD
Hi gmx-users, I want to get a solvent density map like that in the link http://p13.freep.cn/p.aspx?u=v20_p13_p_0902131629052385_0.bmp So I use g_spatial to calculate the spatial distribution function and get a *.cube file. I load the *.cube file into VMD and view it as an volumeslice but no anything is displayed. how can I get the solvent density map? If you have some experience,please give me some suggestion. Jinyao Wang wan...@ciac.jl.cn 2009-02-13 ___ 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] .mdp file for polymer
hello sir, I made nstvout and nstfout parameters to zero and frequency to update position coordinates alone (nstxout) to 1000.But still am getting only one frame when viewed the trajectory in VMD.It is an NVT ensemble.How can i get more than one frame?I think the timestep and nsteps i have given is right only.Please help me out in this issue. ___ 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] Nehalem
Dear All, could somebody already test the performance of Intel's Nehalem CPU in comparison to Harpertown or to AMD's Shanghai using Gromacs? Thanks Rainer __ Dr. Rainer Böckmann Theoretical Computational Membrane Biology Center for Bioinformatics Saar Universität des Saarlandes Gebäude C7.1, EG D-66041 Saarbrücken, Germany Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180 E-Mail: rai...@bioinformatik.uni-saarland.de http://www.bioinf.uni-sb.de/RB/ ___ ___ 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] P-N vector orientation
Hi, as Nicolas suggested you can use my program g_tilt to do such an analysis. Instead of giving the whole backbone as a selection, simply give the 2 atoms (P N). Initially g_tilt uses the first eigen vector of the inertia matrix of the atom selection, so you might want to simplify the code to calculate the PN vector (using [xN-xP,yN-yP,zN-zP]). Ciao, Patrick Nicolas a écrit : Hello, I just remember that you might be interested by g_tilt developed by Patrick Fuchs.: http://www.dsimb.inserm.fr/~fuchs/download/ http://www.dsimb.inserm.fr/%7Efuchs/download/ Its purpose is to calculate the orientation of an helix in a bilayer, however it might tweaked to calculate the NP dipole orientation. I've done that one time, but it was only for a particular lipid in a membrane, not for the whole bilayer. IIRW, the result was the same than the one of my scripts and the calculation was much faster. Nicolas ANINDITA GAYEN a écrit : Dear Xavier Periole I am a GROMACS user, presently working with DMPC bilayer.. I want to calculate the orientation of the head groups P-N vector. From gmx-users, I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now. http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/ ___ 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 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 -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ 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: Nehalem
Hi, Gromacs is a test term of SPEC CPU2006 benchmark suite, which aims at providing a standard and comparable performance evaluation for different platform. They provided a online database http://www.spec.org/cgi-bin/osgresults?conf=cpu2006 visit it and search the CPU name you interested, the performance on gromacs and some other scientific softwares will be listed. The performances record of the CPU based on Harpertown, Shanghai and Nehalem are now available on the database. --Lu Tian Dear All, could somebody already test the performance of Intel's Nehalem CPU in comparison to Harpertown or to AMD's Shanghai using Gromacs? Thanks Rainer __ Dr. Rainer Böckmann Theoretical Computational Membrane Biology Center for Bioinformatics Saar Universität des Saarlandes Gebäude C7.1, EG D-66041 Saarbrücken, Germany Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180 E-Mail: rai...@bioinformatik.uni-saarland.de http://www.bioinf.uni-sb.de/RB/ ___ 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: Nehalem
One point here is the fact that on specfp gromacs is NOT compiled with the assembly parts. Those come from fortran. Performance hit, in different ways from different architectures and compilers due to this. ;) On Fri, Feb 13, 2009 at 10:04 AM, sobereva sobju...@yahoo.com.cn wrote: Hi, Gromacs is a test term of SPEC CPU2006 benchmark suite, which aims at providing a standard and comparable performance evaluation for different platform. They provided a online database http://www.spec.org/cgi-bin/osgresults?conf=cpu2006 visit it and search the CPU name you interested, the performance on gromacs and some other scientific softwares will be listed. The performances record of the CPU based on Harpertown, Shanghai and Nehalem are now available on the database. --Lu Tian Dear All, could somebody already test the performance of Intel's Nehalem CPU in comparison to Harpertown or to AMD's Shanghai using Gromacs? Thanks Rainer __ Dr. Rainer Böckmann Theoretical Computational Membrane Biology Center for Bioinformatics Saar Universität des Saarlandes Gebäude C7.1, EG D-66041 Saarbrücken, Germany Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180 E-Mail: rai...@bioinformatik.uni-saarland.de http://www.bioinf.uni-sb.de/RB/ ___ 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 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] Problem using MPIRUN MDRUN
Dear users, I'm trying to run gromacs v.3.3.3. on a cluster of 4 machines with 8 CPUs each. I've checked the mailing list and the manual in order to find the correct way to write the command line and I've found that the commands listed below are supposed to be correct and to work. grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file_md.tpr -np 32 mpirun -np 32 /dms/prog/bin/mdrun_mpi_d -s file_md.tpr -o file_md.trr -c file_md.gro -np 32 The dynamics starts, but after few minutes it crushes and I've got this message of error: One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 24320 failed on node n0 (195.195.124.134) with exit status 1. Does anyone can help me to sort out this problem?Does anyone know what I'm doing wrong? Thanks a lot, Filippo ___ 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] .mdp file for polymer
varsha gautham wrote: hello sir, I made nstvout and nstfout parameters to zero and frequency to update position coordinates alone (nstxout) to 1000.But still am getting only one frame when viewed the trajectory in VMD. Just like some other trajectory formats, you do have to open a structure file and then import the trajectory... It is an NVT ensemble.How can i get more than one frame?I think the timestep and nsteps i have given is right only.Please help me out in this issue. So what does gmxcheck or gmxdump tell you about your trajectories? 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
RE: [gmx-users] Problem using MPIRUN MDRUN
Hi Filippo, Do you have checked your trajectory ( *.trr or *.xtc) and *.log ? You system may have 'exploded'... Osmair Date: Fri, 13 Feb 2009 13:27:09 + From: fpri...@nimr.mrc.ac.uk To: gmx-users@gromacs.org Subject: [gmx-users] Problem using MPIRUN MDRUN Dear users, I'm trying to run gromacs v.3.3.3. on a cluster of 4 machines with 8 CPUs each. I've checked the mailing list and the manual in order to find the correct way to write the command line and I've found that the commands listed below are supposed to be correct and to work. grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file_md.tpr -np 32 mpirun -np 32 /dms/prog/bin/mdrun_mpi_d -s file_md.tpr -o file_md.trr -c file_md.gro -np 32 The dynamics starts, but after few minutes it crushes and I've got this message of error: One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 24320 failed on node n0 (195.195.124.134) with exit status 1. Does anyone can help me to sort out this problem?Does anyone know what I'm doing wrong? Thanks a lot, Filippo ___ 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 _ Windows Live Messenger. O melhor em multitarefa. http://www.microsoft.com/windows/windowslive/products/messenger.aspx___ 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] Problem using MPIRUN MDRUN
Thanks a lot, I'll check stderr and stdout, because I think that the log file is correct (it looks like a normal dynamic that has been manually interrupted). The system is not exploded cause it does not generate the gro file and step files. ___ 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 get a solvent density map using volumeslice in VMD
Hi Jinyao, your question is not very well defined. It is considerably easier for me if you tell me exactly what you tried to get this to work, which I imagine was more than simply running g_spacial once and selecting the volume_slice representation in vmd. That said, 1. Can you view it as an isosurface? That is a simpler representation to get working and so is a valuable test. 2. Did you try pushing the bar that moves the slicing plane up and down? 2b. Did you try changing the axis and then repeating #2, above? 3. Open the colors dialog and go to color scales. When you see the volume slice as entirely one color, does that color correspond to full strength or no signal? 4. With the color scale mentioned above, try changing the offset and magnitude of the gradient and see if that has any effect. 5. What options did you use when you ran g_spatial? Chris. Message: 1 Date: Fri, 13 Feb 2009 16:43:14 +0800 From: Jinyao Wang wan...@ciac.jl.cn Subject: [gmx-users] how to get a solvent density map using volumeslice inVMD To: gmx-users gmx-users@gromacs.org Message-ID: 434514306.04...@eyou.net Content-Type: text/plain;charset=gb2312 Hi gmx-users, I want to get a solvent density map like that in the link http://p13.freep.cn/p.aspx?u=v20_p13_p_0902131629052385_0.bmp So I use g_spatial to calculate the spatial distribution function and get a *.cube file. I load the *.cube file into VMD and view it as an volumeslice but no anything is displayed. how can I get the solvent density map? If you have some experience,please give me some suggestion. ___ 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] Problem with different version
Hi, I apologize in advance if my question has been asked before. I don't follow all the questions and I am sorry. Recently I have faced problem with g_clustsize command in Gromacs. I've used the command as below and I've gotten the error : g_clustsize_d -f drg -s drg -nc nclut -mc maxclust -ac avclust -cut 0.45 -mol -n drg Reading frame 0 time0.000 Reading file drg.tpr, VERSION 4.0 (single precision) Reading file drg.tpr, VERSION 4.0 (single precision) Using molecules rather than atoms. Not reading index file drg.ndx Last frame 2000 time 2.000 cmid: 1, cmax: 1, max_size: 1 Back Off! I just backed up csize.xpm to ./#csize.xpm.2# --- Program g_clustsize_d, VERSION 4.0 Source code file: matio.c, line: 533 Fatal error: Lo: 0.00, Mid: 1.00, Hi: 1.00 I have done some part of my simulation with the last version and some part with the latest one. So I decided to check whether there is a problem with my new .tpr file. But,when I want to read my new version .tpr file with g_clustsize from old version, it doesn't work. This doesn't make sense for me . I appreciate your help, Shaqayeq ___ 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] Virial from non-bonded forces
Dear David, Thanks for your response. It was very valuable. I looked in the codes to locate the place(s) where GROMACS obtains/accumulates the shifted forces and as far as I could see, GROMACS does this correctly for the short-range forces and re-distributes the forces on the virtual sites unto the real/atomic sites before calculating the virial. For the long-range forces (Ewald, SPME), however, one has to use all the possible (infinite number of) images but GROMACS does not do this; personally, I think it is impossible to do this. There is, however, this important point: if the position of the dummy scales the same way as those of the real sites, then one does not need to re-distribute the forces in order to calculate the virial -- simply treat all sites in the same way. Thus, for dummy types 1,2,3, the virial calculated (even with Ewald) will be correct since r_d(L*r_1, ..., L*r_n) = L*r_d(r_1, ..., r_n) where r_d is the dummy site and r_1, ..., r_n are the real/atomic sites. For types 3fd, 3fad, 3out, and 4fd for which the position of the virtual site does not scale like those of the real sites, the virial calculated in GROMACS will be correct only for the short-range forces (since this is done correctly in the code) but not for the long-range ones. Note, however, that for rigid molecules, since the intramolecular bondlengths are constant, one can replace certain magnitudes |( )| by constants in 3fd, 3fad, and 4fd. [In 3out replace by c/sqrt(|rij| * |rik|) ] so that r_d will scale just like any r_i or any r_ij. Thus, for rigid monomers (eg TIP5P), one again gets the correct contribution to the virial from long-range forces. Fortunately, I do not know any flexible models out there that use 3fd, 3fad, 3out, and 4fd for the virtual sites. Thanks for your time! o. From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, February 10, 2009 12:52:06 PM Subject: Re: [gmx-users] Virial from non-bonded forces Omololu Akin-Ojo wrote: Hi, I have two main issues: 1. In Appendix B of the GROMACS user manual, there is a discussion of the calculation of the virial. The top of the second page of the appendix (just before B.1.2) states, In a triclinic system there are 27 possible images of i, My question is: In this case, there should also be 27 possible forces on particle j due to i. Granted, only the force corresponding to the shortest i-j distance will be non-zero but when the forces are multiplied by \delta_i, (in Eq. B.11) the correct force (out of all the 27 possible ones) should be multiplied by the corresponding \delta_i. In other words, if we label each of the 27 possible \delta_i by n ((\delta_i)^n), we should do the same with the forces F_i ((F_i)^n) and the sum in B.11 should also contain a sum over n. For ver. 3.3.1, I see that in src/mdlib/calcvir.c each of the different (\delta_i)^n is used but for fixed i, the same force F_i is used irrespective of the value of n. (See also, J. Chem. Phys. vol. 117, p2449 (2002), the 3rd line from the bottom of the 2nd column on the first page.) The force on the non+central boxes are also stored separately in an arrya fshift. The displacement part of the position is thus taken care of separately. 2. How does GROMACS calculate the virial for charged virtual sites using the Ewald summation (or SPME)? One needs to redistribute the forces before calculating the virial but if one uses this approach one will need not only 27 possible \delta_i but, technically, an infinite number. The order of redistributing forces and virial calculation is important, and one should indeed do it in the order you describe. This is not completely obvious, since the position used for computing the forces are those of the virtual sites. I do not see why one would need to compute multiple deltas, but it could be that the contribution to fshift (see above) is computed before redistributing the forces, which would not be consistent in that case. GROMACS does reproduce e.g. the density of TIP4P and TIP5P water correctly, so it seems that there is not a large error if there is one at all. Thanks for your input. o. ___ 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 -- 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.
[gmx-users] Langevin Dyanamics in GROMACS
Hi all: Anyone can help me using Langevin Dynamics in GROMACS. Where does the friction coefficient goes and How we can change the forece field to include PMF. Thanks, M. Rahman ___ 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] Langevin Dyanamics in GROMACS
M Hafizur Rahman wrote: Hi all: Anyone can help me using Langevin Dynamics in GROMACS. Where does the friction coefficient goes and How we can change the forece field to include PMF. For Langevin dynamics, read manual sections 3.8 or 3.9, depending on what you want to do. Associated run control parameters are in section 7.3.3, or online: http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html As for PMF, read manual sections 6.1, 6.3, and/or 6.4. -Justin Thanks, M. Rahman ___ 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
Re: [gmx-users] Problem using MPIRUN MDRUN
fpri...@nimr.mrc.ac.uk wrote: Thanks a lot, I'll check stderr and stdout, because I think that the log file is correct (it looks like a normal dynamic that has been manually interrupted). If you've manually interrupted the simulation, then you cannot expect the buffered I/O to be correctly formed. The system is not exploded cause it does not generate the gro file and step files. If there's no final coordinate file (.gro by default), then the simulation did not complete correctly. 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
Re: [gmx-users] SIMULATED ANNEALING
sharada wrote: *Thankyou for the reply Mark. In fact I started another simulated annealing job for my peptide with Tcoupl = Berendsen using the same annealing protocol. I didnot get any warnings. However the temperature increases from 0 to 53K and fluctuates around that through out till the end of the simulation. I am attaching the Averages and RMS values for the various components that its calculating. As you can see the average Temp is around 56 -58. Why is this not increasing beyound that? I would also like to know if the RMS fluctuations are in the required range , further if the system is behaving as an NVE ensemble which I don't intend to do right now what parameters I should correct in order to achieve an NPT ensemble. Density of methanol is maintained, however the box sizes are reduced slightly from (editconf -f 2MLT_pdb2gmx.gro -o 2MLT_box.gro -bt octahedron -box 6.9 6.9 6.9) to the ones as shown below. Kindly guide me through. Read the manual sections in chapter 7 on simulated annealing and temperature coupling, and check carefully how they work and what values you've selected. 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
