[gmx-users] Energy minimization: problems with ramachanrad score
This does not imply that less EM is better than more EM. It implies that the native structure is not necessarily in an absolute energy minimum according to our FF's. This is certainly true. We could take the point of view that when an experimentalist refers to as a native structure is actually a model that fits a particular electron density map and another crystal form is bound to differ, but I guess we all know that our FF's are less accurate than this difference so it's probably a moot point. EM with MM FF's is not rubbish. It's important and it has its place. So randomizing a structure and running EM doesn't take you back to the original minimum? sure, this is why we call the energy surface rugged. To get back to your homology modeling, I would always suspect that you will need to run MD in order to explore conformational space. Homology modeling is not my strong suit, but I've seen cases experimentally where a single amino acid mutation can destabilize a folded protein and cause it to be unfolded (and vice-versa), so in that light I'm still astounded that homology modeling works at all. Sorry to be a little vague, but then again you didn't really ask a specific question, unless plasmatic is a real word... Chris. -- original message -- I 'm trying to relax my homology models from steric clashes, and while searching for the appropriate minimization scheme, I came across this old thread: http://lists.gromacs.org/pipermail/gmx-users/2007-April/027043.html The authors in the cited paper have created near-native structures as a test set with RMSD 1.06 ± 0.14 Å over the native ones. Then they ran energy minimization in vacuo with l-bfgs for 1 steps or until convergence to machine precision and they found that ordinary MM potentials (AMBER99, OPLS-AA, GROMOS96, and ENCAD) showed no significant improvement on the structures. On the contrary the last 3 were found to move the conformation away from the native state by 11%, 40%, and 44% respectively. They also tested their own 3 hybrid Knowledge-Based / Molecular Mechanics (KB/MM) potentials and found that the best performing was moving the structures by 11% closer to the native fold. Essentially they claimed that energy minimization with the ordinary MM potentials is rubbish! I have one remark to make on this. Their decoy set comprised no-native protein conformers with RMSD ~1A. I'm wondering if the results will be similar for RMSDs ~3A as in my case where I'm building homology models with average sequence identity to templates 25-30%? And with respect to the original question, if you overdo it with energy minimization the Ramachandran scores do deteriorate. However if you stop at an intermediate step you can get the same score, bond lengths and angles but with less steric clashes. Is this improvement plasmatic as the authors claim, namely you have moved away from the native fold although stereochemically the model look good? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100617/aafe7f09/attachment.html Previous message: [gmx-users] Electric field, potential, dielectric constant Next message: [gmx-users] Energy minimization: problems with ramachanrad score Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the gmx-users mailing list -- 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: Subject: [gmx-users] error compiling mopac and gromacs
According to the suggestion I have installed the f2c package in my machine.I am unable to find the g2c package. I have included the f2c library by - export LIBS=-lmopac -lf2c. But when I running ./configure --with-qmmm-mopac --disable-float , an error is comming C compiler cannot create executable. The config.log file shows the following section- onfigure:3413: checking for C compiler default output file name configure:3440: cc -I/usr/local/include -DUSE_MOPAC -L/usr/local/lib conftest.c -lmopac -lf2c 5 /usr/lib/gcc/i486-linux-gnu/4.3.3/../../../../lib/libf2c.so: undefined reference to `MAIN__' collect2: ld returned 1 exit status configure:3443: $? = 1 configure:3481: result: configure: failed program was: | /* confdefs.h. */ Please suggest a way out.Subarna Thakur From: Gerrit Groenhof ggro...@gwdg.de To: gmx-users@gromacs.org Sent: Sat, 12 June, 2010 3:36:54 PM Subject: Re: Subject: [gmx-users] error compiling mopac and gromacs Depending on how your libmopac.a was biuld, you need the to include the f2c or g2c library as well. Gerrit Message: 5 Date: Sat, 12 Jun 2010 14:33:02 +0530 (IST) From: subarna thakur thakur.suba...@yahoo.co.in Subject: [gmx-users] error compiling mopac and gromacs To: gmx-users@gromacs.org Message-ID: 371899.78968...@web95516.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi I am trying to link mopac with gromacs in a 32 bit linux machine. I have downloaded the libmopac.a file and kept it under /usr/local/lib. I installed fftw with double precision and then I set the enviornmental variables for linking mopac and gromacs export LDFLAGS=-L/usr/local/lib -Wl,--wrap,__ctype_b export CPPFLAGS=/usr/local/include -DUSE_MOPAC export LIBS=lmopac then I have ran the ./configure --with-qmmm-mopac --disable-float.It seems to run ok.Then I used the make command but an error is comming as follows- /usr/local/lib/libmopac.a(lread.o)(.text+0x160): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x21f): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x296): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x2d0): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x8b2): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0xb05): more undefined references to `__wrap___ctype_b' follow collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/usr/gromacs-4.0.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/gromacs-4.0.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/usr/gromacs-4.0.3/src' make: *** [all-recursive] Error 1 Please suggest where I have gone wrong. Subarna Thakur -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100612/ed0e12b1/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 74, Issue 69 * -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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] Electric field, potential, dielectric constant
Hi, You may want to use a Poisson-Boltzmann solver, e.g., APBS for this purpose. Ran Vladimir Lankevich wrote: Dear Gromacs Users, I have several questions about electrostatics in Gromacs. I am simulating two proteins in water, separated by certain distance, and was interested in their electrostatic interactions. I was wondering if Gromacs can calculate and show me values of electric field or electric potential at any point within the volume. If yes, how can this be done? I looked through the manual and did not find much. I tried using g_potential, but it only gives me ten values for electric field (if I use 10 slices, and particular direction). This confused me, because I thought that in the system each coordinate would have different electric field. How should I interpret the results of g_potential? Also, can I use Gromacs to compute dielectric constant of a particular region within the volume? How can I do that? Thank you very much!! Cheers, Vladimir -- 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] calculate interfacial tension
Hello, I want to calculate the interfacial tension of the oil/water interface . I use 2D periodic boundary along Z axis , I get the interfacialnbsp;teision from the .edr file (namely #Surf*SurfTen), it seems that the Surf*SurfTen is the total tension nbsp;of the two interface ,is it that ?nbsp; Does it has any influence for I use the 2D periodic boundary along Z axis ? nbsp; Waiting fornbsp;your nbsp;reply eagerly. nbsp; Thank you ! nbsp; nbsp;-- 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] constraints bond length vari by 10%
Hi, I did read the Documentation 5 times now, but I still not get is what the shake_tol does tell me. I tried it with 10 values and can't figure out what it does. My CO bonds are constraint. Otherwise I would have bigger variations of the bond length. My .mdp file looks like this constraints = none constraint_algorithm= shake shake_tol = 0.05 unconstrained_start = no My question is more how I can constrain the bond length such that they vary only by a factor of +/- 0.0001. Thanks On Thu, 17 Jun 2010 08:01:04 +1000 Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Sebastian Waltz sebastian.wa...@physik.uni-freiburg.de Date: Thursday, June 17, 2010 2:23 Subject: Re: [gmx-users] constraints bond length vari by 10% To: Discussion list for GROMACS users gmx-users@gromacs.org Hi Mark, what I have written in the .top you can see in my first massage. OK - but my suggestion was that it was put in the wrong *place* and I don't have enough information to say whether that's true. I actually don't know what to write what and in which .itp/.tpr file I have to add something and I also can't find something in the Internet. The documentation for the constraints is just bad. I understand your frustration, but documentation can't anticipate the answer to every question or it would be infinitely long. That fact doesn't make it bad. What the documentation can do is provide general instruction. If my guess is correct, then the worked example of a .top file in Chapter 5 will help you understand where [constraints] needs to go. Specifically, page 109 will point out that #include ffforcefield.itp [ moleculetype ] ... [atoms] ... #include water.itp [system] ... [molecules] ... [constraints] ... won't work. Section 5.5 has a worked example of how to use [settles] which are a kind of constraint, and work the same way. Once you've worked through this information, if you still have a problem with the documention, then a constructive suggestion for improvement would be welcome :-) Mark On Wed, 16 Jun 2010 09:05:20 +1000 Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Sebastian Waltz sebastian.wa...@physik.uni-freiburg.de Date: Tuesday, June 15, 2010 22:09 Subject: [gmx-users] constraints bond length vari by 10% To: gmx-users@gromacs.org Hi all, I added constraints on some bonds in my system by adding [ constraints ] ;ai aj typedistance 40 41 1 0.1230 47 48 1 0.1230 54 55 1 0.1230 61 62 1 0.1230 to me top file (CO double bonds) and in the mdp file constraints = none . I thought this should more or less fix my bond lengths. Nether the less the bond lengths vary by 10%. Did I make something or is it quite normal? What would be the way to fix the bond length so that they vary only by ca. 1%. You're using the right approach, but you've probably not put your [constraints] directive in the right [moleculetype], or used the wrong .top/.itp/.tpr file at some point. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users 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 correct velocities in trajectory file
Dear gmx'ers, I've done a long NVE simulation in vacuo. During this run I had to take care to diminish the total energy drift, so my choice was comm_mode = None Now, analysing a smaller subsystem (solute + shell of solvent) I want to exclude its COM movement. Sorry, I fail to find any instruction how to do it. Extracting the subset with trjconv -f traj.trr -s -n my_index.ndx -o subset.trr -center centers the subsystem well. But as it can be checked with g_traj -f subset.trr -s subset.tpb -n my_index.ndx -ov -ekt -ekr -com the velocities in subset.trr remain unchanged. Ideally I would like, first, to correct the atom velocities to zero COM velocity, and next to correct them to obtain zero angular momentum of my subsystem. Could anyone advise me how to correct properly the velocities in trr-file? Thank you in advance, -- Regards, Dmitri mailto:ddu...@ngs.ru-- 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] Re: His protonation
So is there a way we can make His neutral before running the simulations as in case of NAMD? Rabab Toubar --- On Wed, 6/16/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: [gmx-users] Re: His protonation To: sagar barage sagarbar...@gmail.com, Gromacs Users' List gmx-users@gromacs.org Date: Wednesday, June 16, 2010, 11:59 PM Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. sagar barage wrote: Dear sir, when i was done the MD of crystal structure the both nitrogen of immadazol ring of histidine is protonated which are not protonated in crystal structure. There are no protons in crystal structures. all histidine in structure contain single protonation but some Histidine is double protonated at both nitrogen why this happens in gromacs? Please read the manual information (or pdb2gmx -h) about how pdb2gmx attempts to add hydrogens to the input structure. -Justingm -- Sagar H. Barage sagarbar...@gmail.com mailto:sagarbar...@gmail.com -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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] System net charge
I have noticed that you get the overall charge WHILE you are setting up the system - when using grompp I think. Now if after the mdrun and I want to check the overall charge, how can I possibly do that? I tried the mailing list but didn't find an answer to my question Thanks Rabab Toubar -- 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] System net charge
Rabab Toubar wrote: I have noticed that you get the overall charge WHILE you are setting up the system - when using grompp I think. Now if after the mdrun and I want to check the overall charge, how can I possibly do that? I tried the mailing list but didn't find an answer to my question The net charge of any molecule (if processed by pdb2gmx) is printed in the topology at the end of the [atoms] directive. Otherwise, take note of what grompp tells you and/or log all your output. -Justin Thanks Rabab Toubar -- 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
[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76
On Jun 17, 2010, at 3:42 PM, abdul wadood wrote: Dear Carsten the command which i give is mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s topol.tpr with this command the same error come which is Can not open file: 3: topol.tpr 3: --- Maybe . (the current directory) is not in your path. Either try mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s ./topol.tpr or give the full path name: mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s /absolute/path/to/topol.tpr Carsten -- 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] Enough hydration of the channel
Hi everyone, I have a homology model of a transporter. I want to study the ligand transport through the channel. i have done the following steps. 1. Ligand has docked to the mouth of the channel 2. Inserted the complex in POPC bilayer, then solvated, and equilibrated for 4ns(with position restarint on Protein ligand) 3. Then I saw tht there are very few wtaer inside the pore, Since this channel is an aqueous pore, I have added water to the channel using genbox. 4. Then the complete system equilibrated for pico seconds. 5,in order to select different snap shots for SMD (want to do a multiple SMDs with different starting structures.) I have run 1ns Production run and selected different frames. Suddenly I found that still there is no enough water in the pore, the water is moving away from the channel during step 4 5? How can I solve this problem? Also how will I know how many water molecules will be sufficient for the channel? Thanks for your support. -- Aswathy -- 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] large forces and monstrous water molecules in energy minimization step
Dear GROMACS users, When trying to simulate a pair of interacting proteins in water, I have encountered problems that ultimately resulted in the simulation crashing. I then tried to simplify the system as far as possible while retaining the problem; I now believe the problem (or at least a part of it) lies in the energy minimization step (the first molecular dynamics one). Specifically, the forces encountered during this step are very large, and some water molecules (which are supposed to be rigid) become giant and misshapen. In more details: 1) I use GROMACS version 4.0.7, single precision, on a server with two Intel x86-64 processors and the redhat 5.4 linux OS. 2) I created a PDB file, called NaCl.pdb, with only two atoms, actually Na+ and Cl- ions separated by their distance in the lattice of salt: HET NA A 1 1 HET CL A 1 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 1 NANA 1+ FORMUL 2 CLCL 1- HETATM1 NANA A 1 -1.410.0 0.01.00 0.0 NA HETATM2 CLCL A 1 +1.410.0 0.01.00 0.0 CL 3) I use the tip3p water model: pdb2gmx -f NaCl.pdb -water tip3p 4) I create the box: editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro 5) I add water using spc216, creating the saltwater.gro file (which seems O.K. by inspection): genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro 6) I create the energy minimization parameter file em.mdp: --em.mdp-- integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdwtype = Cut-off rvdw= 1.0 nstenergy = 10 -- 7) I prepare the em.tpr file for the energy minimization run: grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr 8) I run the energy minimization step: mdrun -v -deffnm em 9) Looking at the em.log file I see that this step converged to machine precision but did not have maximal force 10: ... Enabling SPC water optimization for 7561 molecules. ... Max number of connections per atom is 2 Total number of connections is 30244 Max number of graph edges per atom is 2 Total number of graph edges is 30244 Going to use C-settle (7561 waters) wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588 rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572 ... Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 ... Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax 10. Potential Energy = -3.4678925e+05 Maximum force = 6.4623531e+05 on atom 11052 Norm of force = 5.4643726e+03 10) Looking at the em.gro file I see one monstrous water molecule (no. 3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal distance is about 0.1 nm. Its HW2 atom (no. 11054) is close to another water molecule (no. 5849), e.g., 0.047 nm from the latter's HW2 atom (no. 17543): ... 3686SOL OW11052 4.348 3.778 -0.629 3686SOLHW111053 5.360 2.601 0.505 3686SOLHW211054 6.518 1.650 0.861 ... 5849SOL OW17541 6.525 1.698 0.900 5849SOLHW117542 6.606 1.649 0.918 5849SOLHW217543 6.481 1.648 0.832 ... 11) During the simulation, several files called stepnnl.pdb were produced for problematic steps, where nn=11,15,19 and l=b,c. For example, the file step19c.pdb indeed shows a problematic water molecule no. 3686, while step19b.pdb does not. Likewise, the earlier step11c.pdb shows a problematic water molecule no. 3266 while step11b.pdb seems proper. The stdout/stderr of mdrun contains warnings like the following: ... t = 0.019 ps: Water molecule starting at atom 11052 can not be settled. Check for bad contacts and/or reduce the timestep. ... 12) Reducing the neighbor list update time, i.e., setting nstlist = 1, does not produce any change. 13) Trying to use the conjugate gradient integrator instead of steepest descent, i.e., setting integrator = cg, is even worse - the running crashes: ... Step 16, Epot=-1.258771e+35, Fnorm= nan, Fmax= inf (atom 14493) Segmentation fault Exit 139 So, am I doing something wrong? How can I avoid these problems? Thanks, Ehud Schreiber. -- 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] RE: Parallel instalation: gmx-users Digest, Vol 74, Issue 76
Dear Carsten I give the path for the topol.tpr file now the error is change which is Fatal error: 3: Too many LINCS warnings (4254) 3: If you know what you are doing you can adjust the lincs warning threshold in your mdp file 3: or set the environment variable GMX_MAXCONSTRWARN to -1, 3: but normally it is better to fix the problem 3: --- 3: 3: You're About to Hurt Somebody (Jazzy Jeff) 3: 3: Halting program mdrun_mpi 3: 3: gcq#98: You're About to Hurt Somebody (Jazzy Jeff) 3: 3: [0] MPI Abort by user Aborting program ! 3: [0] Aborting program! 3: p4_error: latest msg from perror: No such file or directory Abdul Wadood, Research Scholar, Dr.Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi-75720, Pakistan. Email:wadoodbiochem...@hotmail.com Subject: Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76 From: ckut...@gwdg.de Date: Thu, 17 Jun 2010 15:46:40 +0200 CC: wadoodbiochem...@hotmail.com To: gmx-users@gromacs.org On Jun 17, 2010, at 3:42 PM, abdul wadood wrote:Dear Carsten the command which i give is mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s topol.tpr with this command the same error come which is Can not open file: 3: topol.tpr 3: --- Maybe . (the current directory) is not in your path. Either try mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s ./topol.tpr or give the full path name: mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s /absolute/path/to/topol.tpr Carsten _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3-- 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] large forces and monstrous water molecules in energy minimization step
Use a different box size. I replicated your problem, but your run completes successfully with a box set up with editconf -d 1 instead of -d 3.3. If you set nstxout = 1 during the EM process, you'll see the problematic water molecule become unstable. It looks as if there is a small void in the solvent (due to the way genbox tries to stack solvent configurations) and your water molecule simply can't find a good orientation within that void. -Justin Ehud Schreiber wrote: Dear GROMACS users, When trying to simulate a pair of interacting proteins in water, I have encountered problems that ultimately resulted in the simulation crashing. I then tried to simplify the system as far as possible while retaining the problem; I now believe the problem (or at least a part of it) lies in the energy minimization step (the first molecular dynamics one). Specifically, the forces encountered during this step are very large, and some water molecules (which are supposed to be rigid) become giant and misshapen. In more details: 1) I use GROMACS version 4.0.7, single precision, on a server with two Intel x86-64 processors and the redhat 5.4 linux OS. 2) I created a PDB file, called NaCl.pdb, with only two “atoms”, actually Na+ and Cl- ions separated by their distance in the lattice of salt: HET NA A 1 1 HET CL A 1 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 1 NANA 1+ FORMUL 2 CLCL 1- HETATM1 NANA A 1 -1.410.0 0.01.00 0.0 NA HETATM2 CLCL A 1 +1.410.0 0.01.00 0.0 CL 3) I use the tip3p water model: pdb2gmx -f NaCl.pdb -water tip3p 4) I create the box: editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro 5) I add water using spc216, creating the saltwater.gro file (which seems O.K. by inspection): genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro 6) I create the energy minimization parameter file em.mdp: --em.mdp-- integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdwtype = Cut-off rvdw= 1.0 nstenergy = 10 -- 7) I prepare the em.tpr file for the energy minimization run: grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr 8) I run the energy minimization step: mdrun -v -deffnm em 9) Looking at the em.log file I see that this step converged to machine precision but did not have maximal force 10: … Enabling SPC water optimization for 7561 molecules. … Max number of connections per atom is 2 Total number of connections is 30244 Max number of graph edges per atom is 2 Total number of graph edges is 30244 Going to use C-settle (7561 waters) wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588 rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572 … Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 … Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax 10. Potential Energy = -3.4678925e+05 Maximum force = 6.4623531e+05 on atom 11052 Norm of force = 5.4643726e+03 10) Looking at the em.gro file I see one monstrous water molecule (no. 3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal distance is about 0.1 nm. Its HW2 atom (no. 11054) is close to another water molecule (no. 5849), e.g., 0.047 nm from the latter’s HW2 atom (no. 17543): … 3686SOL OW11052 4.348 3.778 -0.629 3686SOLHW111053 5.360 2.601 0.505 3686SOLHW211054 6.518 1.650 0.861 … 5849SOL OW17541 6.525 1.698 0.900 5849SOLHW117542 6.606 1.649 0.918 5849SOLHW217543 6.481 1.648 0.832 … 11) During the simulation, several files called stepnnl.pdb were produced for problematic steps, where nn=11,15,19 and l=b,c. For example, the file step19c.pdb indeed shows a problematic water molecule no. 3686, while step19b.pdb does not. Likewise, the earlier step11c.pdb shows a problematic water molecule no. 3266 while step11b.pdb seems proper. The stdout/stderr of mdrun contains warnings like the following: … t = 0.019 ps: Water molecule starting at atom 11052 can not be settled. Check for bad contacts and/or reduce the timestep. … 12) Reducing the neighbor list update time, i.e., setting nstlist = 1, does not produce any change. 13) Trying to use the conjugate gradient integrator instead of steepest descent, i.e., setting integrator = cg, is even worse - the running crashes: … Step 16, Epot=-1.258771e+35, Fnorm= nan, Fmax= inf (atom 14493) Segmentation fault Exit 139 So, am I doing something wrong? How can I avoid these problems? Thanks, Ehud Schreiber.
[gmx-users] Enough hydration of the channel
Determining how many waters is sufficient is a tough problem, try successive runs of option #3, below. As for the simpler topic of getting more hydration: 1. If the issue is simply getting the channel hydrated enough to overcome some transition from dry to wet, then run a neat water box od 216 spc for 100 ps and extract a frame every 10 ps, then run genbox 10x successively using each of these frames. This should give you massive hydration. 2. If that doesn't work, then you could add a new equilibration step where you posres some cap waters so that the channel can not dry out. This may allow SC's to equilibrate to a wet environment. 3. If the issue is that the water is still moving out, then why not do SMD on a water into the pore and find out where the repulsion is. -- original message -- Hi everyone, I have a homology model of a transporter. I want to study the ligand transport through the channel. i have done the following steps. 1. Ligand has docked to the mouth of the channel 2. Inserted the complex in POPC bilayer, then solvated, and equilibrated for 4ns(with position restarint on Protein ligand) 3. Then I saw tht there are very few wtaer inside the pore, Since this channel is an aqueous pore, I have added water to the channel using genbox. 4. Then the complete system equilibrated for pico seconds. 5,in order to select different snap shots for SMD (want to do a multiple SMDs with different starting structures.) I have run 1ns Production run and selected different frames. Suddenly I found that still there is no enough water in the pore, the water is moving away from the channel during step 4 5? How can I solve this problem? Also how will I know how many water molecules will be sufficient for the channel? Thanks for your support. -- 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] large forces and monstrous water molecules in energy minimization step
Hi, For the dynamics to work you indeed need smaller forces (on the order of 10^3 in GMX units). Using flexible water molecules I was able to get this for your NaCl model. Just add: define = -DFLEXIBLE To your input. This should work also to fill in the voids I guess. Ran -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- Justin A. Lemkul wrote: Use a different box size. I replicated your problem, but your run completes successfully with a box set up with editconf -d 1 instead of -d 3.3. If you set nstxout = 1 during the EM process, you'll see the problematic water molecule become unstable. It looks as if there is a small void in the solvent (due to the way genbox tries to stack solvent configurations) and your water molecule simply can't find a good orientation within that void. -Justin Ehud Schreiber wrote: Dear GROMACS users, When trying to simulate a pair of interacting proteins in water, I have encountered problems that ultimately resulted in the simulation crashing. I then tried to simplify the system as far as possible while retaining the problem; I now believe the problem (or at least a part of it) lies in the energy minimization step (the first molecular dynamics one). Specifically, the forces encountered during this step are very large, and some water molecules (which are supposed to be rigid) become giant and misshapen. In more details: 1) I use GROMACS version 4.0.7, single precision, on a server with two Intel x86-64 processors and the redhat 5.4 linux OS. 2) I created a PDB file, called NaCl.pdb, with only two “atoms”, actually Na+ and Cl- ions separated by their distance in the lattice of salt: HET NA A 1 1 HET CL A 1 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 1 NANA 1+ FORMUL 2 CLCL 1- HETATM1 NANA A 1 -1.410.0 0.01.00 0.0 NA HETATM2 CLCL A 1 +1.410.0 0.01.00 0.0 CL 3) I use the tip3p water model: pdb2gmx -f NaCl.pdb -water tip3p 4) I create the box: editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro 5) I add water using spc216, creating the saltwater.gro file (which seems O.K. by inspection): genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro 6) I create the energy minimization parameter file em.mdp: --em.mdp-- integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdwtype = Cut-off rvdw= 1.0 nstenergy = 10 -- 7) I prepare the em.tpr file for the energy minimization run: grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr 8) I run the energy minimization step: mdrun -v -deffnm em 9) Looking at the em.log file I see that this step converged to machine precision but did not have maximal force 10: … Enabling SPC water optimization for 7561 molecules. … Max number of connections per atom is 2 Total number of connections is 30244 Max number of graph edges per atom is 2 Total number of graph edges is 30244 Going to use C-settle (7561 waters) wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588 rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572 … Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 … Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax 10. Potential Energy = -3.4678925e+05 Maximum force = 6.4623531e+05 on atom 11052 Norm of force = 5.4643726e+03 10) Looking at the em.gro file I see one monstrous water molecule (no. 3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal distance is about 0.1 nm. Its HW2 atom (no. 11054) is close to another water molecule (no. 5849), e.g., 0.047 nm from the latter’s HW2 atom (no. 17543): … 3686SOL OW11052 4.348 3.778 -0.629 3686SOLHW111053 5.360 2.601 0.505 3686SOLHW211054 6.518 1.650 0.861 … 5849SOL OW17541 6.525 1.698 0.900 5849SOLHW117542 6.606 1.649 0.918 5849SOLHW217543 6.481 1.648 0.832 … 11) During the simulation, several files called stepnnl.pdb were produced for problematic steps, where nn=11,15,19 and l=b,c. For example, the file step19c.pdb indeed shows a problematic water molecule no. 3686, while step19b.pdb does not. Likewise, the earlier step11c.pdb shows
[gmx-users] [pairs] and [dihedrals]
Hi everyone, I have one question about topology, If I want to write topology by hand, how can I write pairs and dihedrals without mistakes? Is there any free softwares to use? Thank you _ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969-- 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] [pairs] and [dihedrals]
you zou wrote: Hi everyone, I have one question about topology, If I want to write topology by hand, how can I write pairs and dihedrals without mistakes? Is there any free softwares to use? If you're using some automated program, then you're not doing it by hand :) There are several on the Gromacs' User Contribution site. There is no substitute for understanding the intrinsics of your desired force field and how it treats these terms, as well as Chapter 5 of the Gromacs manual. Understanding all of this is the only way to not make mistakes (being careful of course to properly implement all that you have learned from your reading). -Justin Thank you Hotmail: Free, trusted and rich email service. Get it now. https://signup.live.com/signup.aspx?id=60969 -- 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
[gmx-users] Incomplete ring
Hi Users, I have a .pdb file, in this file when I want to use pdb2gmx command there is this error massage:Fatal error:Incomplete ring in HIS680 this aminoacid is not complete in general, I don't know how can I complete this such that I don't add HIS for complete? Please give me a hint. Thank you _ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969-- 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] Incomplete ring
On 2010-06-17 21.06, you zou wrote: Hi Users, I have a .pdb file, in this file when I want to use pdb2gmx command there is this error massage: Fatal error: Incomplete ring in HIS680 this aminoacid is not complete in general, I don't know how can I complete this such that I don't add HIS for complete? Please give me a hint. add the missing atoms with emacs (or another text editor). Then minimize. Thank you Hotmail: Free, trusted and rich email service. Get it now. https://signup.live.com/signup.aspx?id=60969 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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
Re: [gmx-users] constraints bond length vari by 10%
- Original Message - From: Sebastian Waltz sebastian.wa...@physik.uni-freiburg.de Date: Thursday, June 17, 2010 18:59 Subject: Re: [gmx-users] constraints bond length vari by 10% To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, I did read the Documentation 5 times now, but I still not get is what the shake_tol does tell me. I tried it with 10 values and can't figure out what it does. My CO bonds are constraint. Otherwise I would have bigger variations of the bond length. My .mdp file looks like this constraints = none constraint_algorithm= shake shake_tol = 0.05 unconstrained_start = no My question is more how I can constrain the bond length such that they vary only by a factor of +/- 0.0001. The above is fine, except that your topology probably has no constraints defined in it, because your [constraints] is in the wrong place. Try commenting out the contents of your constraints directive and see if you get identical results. This is the last time I'm going to repeat myself, since you're appearing to ignore my feedback :-) Mark On Thu, 17 Jun 2010 08:01:04 +1000 Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Sebastian Waltz sebastian.wa...@physik.uni-freiburg.de Date: Thursday, June 17, 2010 2:23 Subject: Re: [gmx-users] constraints bond length vari by 10% To: Discussion list for GROMACS users gmx-users@gromacs.org Hi Mark, what I have written in the .top you can see in my first massage. OK - but my suggestion was that it was put in the wrong *place* and I don't have enough information to say whether that's true. I actually don't know what to write what and in which .itp/.tpr file I have to add something and I also can't find something in the Internet. The documentation for the constraints is just bad. I understand your frustration, but documentation can't anticipate the answer to every question or it would be infinitely long. That fact doesn't make it bad. What the documentation can do is provide general instruction. If my guess is correct, then the worked example of a .top file in Chapter 5 will help you understand where [constraints] needs to go. Specifically, page 109 will point out that #include ffforcefield.itp [ moleculetype ] ... [atoms] ... #include water.itp [system] ... [molecules] ... [constraints] ... won't work. Section 5.5 has a worked example of how to use [settles] which are a kind of constraint, and work the same way. Once you've worked through this information, if you still have a problem with the documention, then a constructive suggestion for improvement would be welcome :-) Mark On Wed, 16 Jun 2010 09:05:20 +1000 Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Sebastian Waltz sebastian.wa...@physik.uni-freiburg.de Date: Tuesday, June 15, 2010 22:09 Subject: [gmx-users] constraints bond length vari by 10% To: gmx-users@gromacs.org Hi all, I added constraints on some bonds in my system by adding [ constraints ] ;ai aj typedistance 40 41 1 0.1230 47 48 1 0.1230 54 55 1 0.1230 61 62 1 0.1230 to me top file (CO double bonds) and in the mdp file constraints = none . I thought this should more or less fix my bond lengths. Nether the less the bond lengths vary by 10%. Did I make something or is it quite normal? What would be the way to fix the bond length so that they vary only by ca. 1%. You're using the right approach, but you've probably not put your [constraints] directive in the right [moleculetype], or used the wrong .top/.itp/.tpr file at some point. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users 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
[gmx-users] git
Hi, This is the first time I am using git. I tried to get started by using - git clone git://git.gromacs.org/gromacs.git - command but got an error - command not found: git (I have tried different versions of this command available with the same result). I am sure this is something extremely trivial. Can someone let me know what am I doing wrong? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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] git
Sai Pooja wrote: Hi, This is the first time I am using git. I tried to get started by using - git clone git://git.gromacs.org/gromacs.git http://git.gromacs.org/gromacs.git - command but got an error - command not found: git (I have tried different versions of this command available with the same result). I am sure this is something extremely trivial. Can someone let me know what am I doing wrong? Have you actually installed git? If so, it may just not be in your $PATH. If not, install it before you try to use it :) -Justin Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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
Re: [gmx-users] Enough hydration of the channel
Thank you very much. In some papers I have seen the graph for hydration of the channel. How can we calculate that using Gromacs ? (or any other program?) Regards, -Aswathy On Thu, Jun 17, 2010 at 7:52 PM, chris.ne...@utoronto.ca wrote: Determining how many waters is sufficient is a tough problem, try successive runs of option #3, below. As for the simpler topic of getting more hydration: 1. If the issue is simply getting the channel hydrated enough to overcome some transition from dry to wet, then run a neat water box od 216 spc for 100 ps and extract a frame every 10 ps, then run genbox 10x successively using each of these frames. This should give you massive hydration. 2. If that doesn't work, then you could add a new equilibration step where you posres some cap waters so that the channel can not dry out. This may allow SC's to equilibrate to a wet environment. 3. If the issue is that the water is still moving out, then why not do SMD on a water into the pore and find out where the repulsion is. -- original message -- Hi everyone, I have a homology model of a transporter. I want to study the ligand transport through the channel. i have done the following steps. 1. Ligand has docked to the mouth of the channel 2. Inserted the complex in POPC bilayer, then solvated, and equilibrated for 4ns(with position restarint on Protein ligand) 3. Then I saw tht there are very few wtaer inside the pore, Since this channel is an aqueous pore, I have added water to the channel using genbox. 4. Then the complete system equilibrated for pico seconds. 5,in order to select different snap shots for SMD (want to do a multiple SMDs with different starting structures.) I have run 1ns Production run and selected different frames. Suddenly I found that still there is no enough water in the pore, the water is moving away from the channel during step 4 5? How can I solve this problem? Also how will I know how many water molecules will be sufficient for the channel? Thanks for your support. -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Aswathy -- 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] Enough hydration of the channel
Thanks a lot. On Fri, Jun 18, 2010 at 9:30 AM, Justin A. Lemkul jalem...@vt.edu wrote: Aswathy wrote: Thank you very much. In some papers I have seen the graph for hydration of the channel. How can we calculate that using Gromacs ? (or any other program?) Have a look at some of Oliver Beckstein's programs: http://sbcb.bioch.ox.ac.uk/oliver/software/ There are several that might be useful to you. -Justin Regards, -Aswathy On Thu, Jun 17, 2010 at 7:52 PM, chris.ne...@utoronto.ca mailto: chris.ne...@utoronto.ca wrote: Determining how many waters is sufficient is a tough problem, try successive runs of option #3, below. As for the simpler topic of getting more hydration: 1. If the issue is simply getting the channel hydrated enough to overcome some transition from dry to wet, then run a neat water box od 216 spc for 100 ps and extract a frame every 10 ps, then run genbox 10x successively using each of these frames. This should give you massive hydration. 2. If that doesn't work, then you could add a new equilibration step where you posres some cap waters so that the channel can not dry out. This may allow SC's to equilibrate to a wet environment. 3. If the issue is that the water is still moving out, then why not do SMD on a water into the pore and find out where the repulsion is. -- original message -- Hi everyone, I have a homology model of a transporter. I want to study the ligand transport through the channel. i have done the following steps. 1. Ligand has docked to the mouth of the channel 2. Inserted the complex in POPC bilayer, then solvated, and equilibrated for 4ns(with position restarint on Protein ligand) 3. Then I saw tht there are very few wtaer inside the pore, Since this channel is an aqueous pore, I have added water to the channel using genbox. 4. Then the complete system equilibrated for pico seconds. 5,in order to select different snap shots for SMD (want to do a multiple SMDs with different starting structures.) I have run 1ns Production run and selected different frames. Suddenly I found that still there is no enough water in the pore, the water is moving away from the channel during step 4 5? How can I solve this problem? Also how will I know how many water molecules will be sufficient for the channel? Thanks for your support. -- 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 thewww 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 -- Aswathy -- 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 -- Aswathy -- 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] git
Thanks Justin. I installed git first and then used git clone g...@git.gromacs.org:gromacs.git and this is what I get Initialized empty Git repository in /fs/home/sm868/gromacs/.git/ The authenticity of host 'git.gromacs.org (130.237.163.208)' can't be established. RSA key fingerprint is ef:9e:30:0e:8c:3c:70:27:c9:d5:10:26:3e:4d:a7:08. Are you sure you want to continue connecting (yes/no)? yes Warning: Permanently added 'git.gromacs.org,130.237.163.208' (RSA) to the list of known hosts. g...@git.gromacs.org's password: 1) Empty repository - what does that mean? 2) What password do I need to enter here? Pooja On Thu, Jun 17, 2010 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, This is the first time I am using git. I tried to get started by using - git clone git://git.gromacs.org/gromacs.git http://git.gromacs.org/gromacs.git - command but got an error - command not found: git (I have tried different versions of this command available with the same result). I am sure this is something extremely trivial. Can someone let me know what am I doing wrong? Have you actually installed git? If so, it may just not be in your $PATH. If not, install it before you try to use it :) -Justin Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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 -- Quaerendo Invenietis-Seek and you shall discover. -- 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] git
- Original Message - From: Sai Pooja saipo...@gmail.com Date: Friday, June 18, 2010 15:28 Subject: Re: [gmx-users] git To: Discussion list for GROMACS users gmx-users@gromacs.org Thanks Justin. I installed git first and then used git clone g...@git.gromacs.org:gromacs.git and this is what I get Initialized empty Git repository in /fs/home/sm868/gromacs/.git/ The authenticity of host 'git.gromacs.org (130.237.163.208)' can't be established. RSA key fingerprint is ef:9e:30:0e:8c:3c:70:27:c9:d5:10:26:3e:4d:a7:08. Are you sure you want to continue connecting (yes/no)? yes Warning: Permanently added 'git.gromacs.org,130.237.163.208' (RSA) to the list of known hosts. g...@git.gromacs.org's password: 1) Empty repository - what does that mean? Empty is what you call something before you put something in it :-) 2) What password do I need to enter here? Your approach won't work unless you have a registered .ssh key for g...@git.gromacs.org, i.e. you have permission to write to the repository. The first three different places I looked on the wiki for how to get the git repository recommended a different approach from yours. See http://www.gromacs.org/Developer_Zone/Git. There's a lot of useful git help on the wiki and the web - please use it. Mark On Thu, Jun 17, 2010 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, This is the first time I am using git. I tried to get started by using - git clone git://git.gromacs.org/gromacs.git http://git.gromacs.org/gromacs.git - command but got an error - command not found: git (I have tried different versions of this command available with the same result). I am sure this is something extremely trivial. Can someone let me know what am I doing wrong? Have you actually installed git? If so, it may just not be in your $PATH. If not, install it before you try to use it :) -Justin Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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 -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] git
Shouldn't you just do it anonymously? git clone git://git.gromacs.org/gromacs.git Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of 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. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Sai Pooja Sent: Friday, 18 June 2010 3:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] git Thanks Justin. I installed git first and then used git clone g...@git.gromacs.org:gromacs.git and this is what I get Initialized empty Git repository in /fs/home/sm868/gromacs/.git/ The authenticity of host 'git.gromacs.org (130.237.163.208)' can't be established. RSA key fingerprint is ef:9e:30:0e:8c:3c:70:27:c9:d5:10:26:3e:4d:a7:08. Are you sure you want to continue connecting (yes/no)? yes Warning: Permanently added 'git.gromacs.org,130.237.163.208' (RSA) to the list of known hosts. g...@git.gromacs.org's password: 1) Empty repository - what does that mean? 2) What password do I need to enter here? Pooja On Thu, Jun 17, 2010 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, This is the first time I am using git. I tried to get started by using - git clone git://git.gromacs.org/gromacs.git http://git.gromacs.org/gromacs.git - command but got an error - command not found: git (I have tried different versions of this command available with the same result). I am sure this is something extremely trivial. Can someone let me know what am I doing wrong? Have you actually installed git? If so, it may just not be in your $PATH. If not, install it before you try to use it :) -Justin Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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 -- Quaerendo Invenietis-Seek and you shall discover. -- 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] error in linking mopac and gromacs
According to the suggestion I have installed the f2c package in my machine.I am unable to find the g2c package. I have included the f2c library by - export LIBS=-lmopac -lf2c. But when I running ./configure --with-qmmm-mopac --disable-float , an error is comming C compiler cannot create executable. The config.log file shows the following section- onfigure:3413: checking for C compiler default output file name configure:3440: cc -I/usr/local/include -DUSE_MOPAC -L/usr/local/lib conftest.c -lmopac -lf2c 5 /usr/lib/gcc/i486-linux-gnu/4.3.3/../../../../lib/libf2c.so: undefined reference to `MAIN__' collect2: ld returned 1 exit status configure:3443: $? = 1 configure:3481: result: configure: failed program was: | /* confdefs.h. */ Please suggest a way out.Subarna Thakur -- 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
