Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5
Thank you Mark for your answer! I agree with you when you say that the high pressure is not itself a problem. To avoid that problem I change my system from 1000 molecules to 27000 molecules, and the pressure change from several thousands to several hundreds bar. What I found very strange was the increasing volume (and pressure). My system is very unstable, I know, because the density is very low, and not the opposite, so I was expecting to see the box getting smaller. Looking to the trajectory I can see a box almost empty (with empty I mean empty space, with chloroform molecules aggregating in small droplets), and that's why I found the system behavior very strange. I will follow your suggestion concerning nsttcouple and nstpcouple and the other initial conditions. Nuno Azoia On Wed, Oct 12, 2011 at 6:24 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/10/2011 2:22 AM, Nuno Azoia wrote: Hello! I found something very strange while making a CHCl3 box using gromacs-4.5.5. A look the mailing list, the manual and some release notes for gromacs-4.5 and I couldn't found the answer for my problem. It's possible that I'm doing something wrong, but I can not find what, so I'm describe my problem. I start a chloroform box from scratch, using genconf, and I get o chloroform box with 1000 molecules. I get energy minimization without problems. Then I've run some equilibration steps in a NVT ensemble and in the end I get pressure in the order of hundreds of bar. The high pressure is not itself a problem - small numbers of molecules and short simulation times lead to doubtful statistics for pressure. Then I change to NPT conditions and both the pressure and the volume keep increasing with time. Be sure to visualize your trajectory to confirm its behaviour matches what you expect from the trends in P and V. To discard the possibility of a size problem, I repeat everything with a box of 27000 molecules, with a volume of ~13800 nm^3. The problem was the same. Very high pressures (150-200 bar) and very low densities ( 200 g/L) after 750 ps simulation time. And both volume and pressure increasing with time. I'm doing now the same procedure, but using gromacs-4.0.7 and I'm getting very different (and better) results. After energy minimization I run 5 steps in a nvt ensemble and I got pressure around -30 bar (Ok for me). After that I start to run the simulations in npt ensemble and the pressure start to increase slowly, with negative values because the system have very low densities (~400 g/L), and the volume is decreasing. So I'm getting the normal reaction from the system. Where is the problem? There are some different parameters to set in the mdp file and I didn't realize that, or is this a problem in gromacs-4.5? It seems you are generating some numerical instability with your choice of initial and simulation conditions, and that gromacs-4.0 was luckier in avoiding the problem. If this is a parallel simulation, then the way communication is managed in order to organize T and P coupling changed going up to 4.5. For equilibration, I would encourage setting nsttcouple and nstpcouple to 1. Using a shorter time step can help with numerical instability. Berendsen T coupling or a larger coupling time constant might also help. After gentler NVT, then switch to NPT, let the box size stabilize, and finally move to larger coupling periods, time steps and v-rescale T coupling. Mark In both cases I used this parameters: - integrator = md dt = 0.002 nsteps = 5 nstcomm = 1 nstxtcout = 500 xtc-precision = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 5 ns_type = grid ;Reaction field rlist = 0.8 coulombtype = Reaction-field rcoulomb = 1.4 epsilon_r = 1.0 epsilon_rf = 4.8 vdwtype = cut-off rvdw = 1.4 ; temperature coupling Tcoupl = v-rescale tc-grps = CHCL3 tau_t = 0.05 ld_seed = -1 ref_t = 300 ; Energy monitoring energygrps = CHCl3 ; Isotropic pressure Pcoupl = no Pcoupltype = isotropic 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 gen_seed = -1 constraint_algorithm=lincs lincs_order = 4 lincs-warnangle = 90 constraints = all-bonds and of course, for the npt ensemble I just change _
[gmx-users] R: Re: H-bond lifetime with g_hbond
Dear all, any other suggestions on how to operate with g_hbond in order to allow convergence of the autocorrelation function (see message below)? Moreover, I have another question. On the same trajectories, I'm using g_hbonds also to infer the contacts between the protein and the ligand (and possibly infer van der Waals interactions). This is the command I used: g_hbond -f protein-GLA_mdC.xtc -s protein-GLA_md.tpr -g protein-GLA_md_vdw.log -contact -r 1.4 -num protein-GLA_md_vdwnum.xvg The printout of the command is: Select a group: 1 Selected 1: 'Protein' Select a group: 15 Selected 15: 'GLA' Checking for overlap in atoms between Protein and GLA Calculating contacts between Protein (5935 atoms) and GLA (24 atoms) Found 24 donors and 5935 acceptors Making hbmap structure...done. Reading frame 0 time0.000 Will do grid-seach on 6x6x4 grid, rcut=1.4 Last frame 3000 time 3.000 Found 38017 different contacts in trajectory Found 0 different atom-pairs within hydrogen bonding distance Average number of contacts per timeframe 0.000 out of 71220 possible However, the .log file gives me a list of interactions such as: # Donor Hydrogen Acceptor GLA395O4 PRO35O GLA395O4 GLY36N GLA395O4 GLY36CA GLA395O4 GLY36HA1 GLA395O4 GLY36HA2 GLA395O4 GLY36C GLA395O4 GLY36O GLA395O4 ARG37N GLA395O4 ARG37H Moreover, I found previously several hBonds in this trajectory, therefore, I don't understand why the printout tells Found 0 different atom-pairs within hydrogen bonding distance and Average number of contacts per timeframe 0.000 out of 71220 possible. I also used flag -r2 instead of -r, but the result is the same. Maybe this is a trivial question, but...what is the correct way to use the flags -contact and -r (or -r2) within g_hbond command? Thanks a lot Anna Message: 1 Date: Tue, 11 Oct 2011 10:25:32 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] H-bond lifetime with g_hbond To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e9451dc.6010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, I have a protein with 5 different ligands. For each system I made 30ns simulation and I calculated the lifetime of the H-bonds between protein and ligand with the command: g_hbond -f traj.xtc -s topol.tpr -hbm hbmap.xpm -hbn hbond.ndx -ac hbac.xvg -life hblife.xvg During all calculations, the printout of the command gave the same warning: WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 and as a matter of fact, the tail of C(t) (average C(t) over second half of acf) reported below this warning was always 0.001, generally comprised between 0.45 and 0.74 with two exceptions: a value of 0.02+/-0.03 and a value of 0.04+/-0.01. The warning doesn't complain about the value of C(t), it is telling you that the standard deviation in the value is unacceptable. Therefore, I'm asking if the forward values considered as lifetimes are reliable or not, and in case, what can I do to avoid this warning. I can't directly comment on this, but it would seems as if the values are not adequately converged. -Justin Thank you very much and best regards Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it mailto:anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5
On 12/10/2011 8:04 PM, Nuno Azoia wrote: Thank you Mark for your answer! I agree with you when you say that the high pressure is not itself a problem. To avoid that problem I change my system from 1000 molecules to 27000 molecules, and the pressure change from several thousands to several hundreds bar. What I found very strange was the increasing volume (and pressure). My system is very unstable, I know, because the density is very low, and not the opposite, so I was expecting to see the box getting smaller. Looking to the trajectory I can see a box almost empty (with empty I mean empty space, with chloroform molecules aggregating in small droplets), and that's why I found the system behavior very strange. Sounds like your initial density might be far too low. grompp reports it, so do check. Mark I will follow your suggestion concerning nsttcouple and nstpcouple and the other initial conditions. Nuno Azoia On Wed, Oct 12, 2011 at 6:24 AM, Mark Abrahammark.abra...@anu.edu.au wrote: On 12/10/2011 2:22 AM, Nuno Azoia wrote: Hello! I found something very strange while making a CHCl3 box using gromacs-4.5.5. A look the mailing list, the manual and some release notes for gromacs-4.5 and I couldn't found the answer for my problem. It's possible that I'm doing something wrong, but I can not find what, so I'm describe my problem. I start a chloroform box from scratch, using genconf, and I get o chloroform box with 1000 molecules. I get energy minimization without problems. Then I've run some equilibration steps in a NVT ensemble and in the end I get pressure in the order of hundreds of bar. The high pressure is not itself a problem - small numbers of molecules and short simulation times lead to doubtful statistics for pressure. Then I change to NPT conditions and both the pressure and the volume keep increasing with time. Be sure to visualize your trajectory to confirm its behaviour matches what you expect from the trends in P and V. To discard the possibility of a size problem, I repeat everything with a box of 27000 molecules, with a volume of ~13800 nm^3. The problem was the same. Very high pressures (150-200 bar) and very low densities (200 g/L) after 750 ps simulation time. And both volume and pressure increasing with time. I'm doing now the same procedure, but using gromacs-4.0.7 and I'm getting very different (and better) results. After energy minimization I run 5 steps in a nvt ensemble and I got pressure around -30 bar (Ok for me). After that I start to run the simulations in npt ensemble and the pressure start to increase slowly, with negative values because the system have very low densities (~400 g/L), and the volume is decreasing. So I'm getting the normal reaction from the system. Where is the problem? There are some different parameters to set in the mdp file and I didn't realize that, or is this a problem in gromacs-4.5? It seems you are generating some numerical instability with your choice of initial and simulation conditions, and that gromacs-4.0 was luckier in avoiding the problem. If this is a parallel simulation, then the way communication is managed in order to organize T and P coupling changed going up to 4.5. For equilibration, I would encourage setting nsttcouple and nstpcouple to 1. Using a shorter time step can help with numerical instability. Berendsen T coupling or a larger coupling time constant might also help. After gentler NVT, then switch to NPT, let the box size stabilize, and finally move to larger coupling periods, time steps and v-rescale T coupling. Mark In both cases I used this parameters: - integrator = md dt= 0.002 nsteps = 5 nstcomm = 1 nstxtcout = 500 xtc-precision = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 5 ns_type = grid ;Reaction field rlist = 0.8 coulombtype = Reaction-field rcoulomb= 1.4 epsilon_r = 1.0 epsilon_rf = 4.8 vdwtype = cut-off rvdw= 1.4 ; temperature coupling Tcoupl = v-rescale tc-grps = CHCL3 tau_t = 0.05 ld_seed = -1 ref_t = 300 ; Energy monitoring energygrps = CHCl3 ; Isotropic pressure Pcoupl = no Pcoupltype = isotropic 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 gen_seed= -1 constraint_algorithm=lincs lincs_order = 4 lincs-warnangle = 90 constraints = all-bonds and of course, for the npt ensemble I just
[gmx-users] Umbrella sampling COM distance
Dear Gromacs Users, I am trying to study the free energy of binding in a protein-ligand complex. I use the following pull input in my mdp file: ; Pull code pull = umbrella pull_geometry = distance pull_dim = N Y N pull_start = yes pull_ngroups = 1 pull_group0 = Protein pull_group1 = GLC pull_rate1 = 0.005 pull_k1 = 1000 if I am pulling in 'Y' direction, is it necessary to make sure that the distance between the COM (of the protein and ligand) = distance between the Y coordinates, i.eY(pro)-Y(lig), ? VMD commands set pro [atomselect top protein] set glc [atomselect top resname GLC] set A [measure center $pro weight mass] 40.33518600463867 35.01163101196289 38.7291374206543 set B [measure center $glc weight mass] 40.591331481933594 39.440189361572266 38.494876861572266 vecdist $A $B 4.4421411021009884 Y(pro)-Y(lig) = 4.42855835 Best, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5
I know that from the beginning. That's why I found very strange the increasing on the system volume. My initial setup have a density of ~400g/L, and for liquid chloroform is ~1400g/L. Using gromacs-4.5 I get densities of about 200 after 750ps simulation time, and using 4.0 I get almost 500 after 1ns. And I was using such low densities because I build the box using genconf with the options -nbox and -dist, starting with one molecule of chloroform. If I used small distance values I get LINCS warnings in the energy minimization step. Using genbox to solvate one empty box with chloroform, I get very strange behaviors, with a very large amount of molecule overlap. But as you said before, I now think that this should be also a paralelization problem, not to mention the numerical instability caused by this very low density. And I think this is a paralelization problem associated with this numerical instability judging from the system behavior. In 4.5, using the option -nt in mdrun, I get some small droplets of liquid chloroform, and in 4.0, using mpi, I get one large droplet of chloroform. It looks like if 4.5 is treating the system like independent small systems, while 4.0 is able to divide the system into small, but interdependent systems. On Wed, Oct 12, 2011 at 12:26 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/10/2011 8:04 PM, Nuno Azoia wrote: Thank you Mark for your answer! I agree with you when you say that the high pressure is not itself a problem. To avoid that problem I change my system from 1000 molecules to 27000 molecules, and the pressure change from several thousands to several hundreds bar. What I found very strange was the increasing volume (and pressure). My system is very unstable, I know, because the density is very low, and not the opposite, so I was expecting to see the box getting smaller. Looking to the trajectory I can see a box almost empty (with empty I mean empty space, with chloroform molecules aggregating in small droplets), and that's why I found the system behavior very strange. Sounds like your initial density might be far too low. grompp reports it, so do check. Mark I will follow your suggestion concerning nsttcouple and nstpcouple and the other initial conditions. Nuno Azoia On Wed, Oct 12, 2011 at 6:24 AM, Mark Abrahammark.abra...@anu.edu.au wrote: On 12/10/2011 2:22 AM, Nuno Azoia wrote: Hello! I found something very strange while making a CHCl3 box using gromacs-4.5.5. A look the mailing list, the manual and some release notes for gromacs-4.5 and I couldn't found the answer for my problem. It's possible that I'm doing something wrong, but I can not find what, so I'm describe my problem. I start a chloroform box from scratch, using genconf, and I get o chloroform box with 1000 molecules. I get energy minimization without problems. Then I've run some equilibration steps in a NVT ensemble and in the end I get pressure in the order of hundreds of bar. The high pressure is not itself a problem - small numbers of molecules and short simulation times lead to doubtful statistics for pressure. Then I change to NPT conditions and both the pressure and the volume keep increasing with time. Be sure to visualize your trajectory to confirm its behaviour matches what you expect from the trends in P and V. To discard the possibility of a size problem, I repeat everything with a box of 27000 molecules, with a volume of ~13800 nm^3. The problem was the same. Very high pressures (150-200 bar) and very low densities ( 200 g/L) after 750 ps simulation time. And both volume and pressure increasing with time. I'm doing now the same procedure, but using gromacs-4.0.7 and I'm getting very different (and better) results. After energy minimization I run 5 steps in a nvt ensemble and I got pressure around -30 bar (Ok for me). After that I start to run the simulations in npt ensemble and the pressure start to increase slowly, with negative values because the system have very low densities (~400 g/L), and the volume is decreasing. So I'm getting the normal reaction from the system. Where is the problem? There are some different parameters to set in the mdp file and I didn't realize that, or is this a problem in gromacs-4.5? It seems you are generating some numerical instability with your choice of initial and simulation conditions, and that gromacs-4.0 was luckier in avoiding the problem. If this is a parallel simulation, then the way communication is managed in order to organize T and P coupling changed going up to 4.5. For equilibration, I would encourage setting nsttcouple and nstpcouple to 1. Using a shorter time step can help with numerical instability. Berendsen T coupling or a larger coupling time constant might also help. After gentler NVT, then switch to NPT, let the box size stabilize, and finally move to larger coupling periods, time steps and v-rescale T coupling. Mark In
Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?
Dear Stephan, Radeons work as well. You can put a 3-4 GPU board together with the highest end AMD or Intel chip for 3K, plus 16G RAM if you look around for a day or two, but the cooling is the main problem (with 1/4 the price radeons Vs. GTI cards), so one has to take cooling into account (h20 cost another 800$, or investing in 4-6 good fans/cooling an additional 2-300$). If you have a slightly higher budget you can get multi CPU boards with 4 GPU slots, ie 4 or 8 CPU's (direct via mail from Taiwan), but the CPU's and GPU's is where the money is spent. No, Radeons don't work and won't work in the near future - Gromacs doesn't support OpenCL. Cooling needs attention, but in reality it's nowhere near $2-300 extra - unless you want the fans with funky leds. Btw, what software is the above hardware description targeting? To me it sounds more like a gaming rig and not something specifically aiming at maximum performance with Gromacs 4.5 (nor 4.6 which is yet to be released). As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon 5900 series (double percission, single is supposed to run around 4 tera flops per GPU, so depends on your needs, desires as far as simulations), and the latest Intel 970's are around 400-500 Gflops/chip. Again, I might be missing something, but how exactly does Gromacs run on Radeons? I assume when referring to the i7 970 (?) above you meant 40-50 GFlops/chip - the i7 970 should have 70 GFlops peak. Also note that Flops are not every useful, what matters is time to solution for the specific problem one wants to solve. Cheers, -- Szilárd -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Uniform Distribution of drug molecules inside water spc216
Dear GMX users Good day to you I have some drug molecules (cisplatin) added manually and randomly inside a system which is going to be solvated in spc216 water. I used genbox command to add the correct number of water molecules needed to solvate the box. The drug molecules are located very closed to each other. Kindly, would you please let me know how I can distribute drug molecules uniformly among the water molecoules to obtain a certain concentration of the drug? May I know if there is any specific tool or script which can help me to do it? Thank you very much Kind regards Meisam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Potential Energy Landscape
I was recently told in passing that it would be possible to construct a 'potential energy landscape' from the simulations I have performed. This way I could remove any loading rate differences between simulations and experimental force experiments I've been performing ... however I cannot find anywhere in which this is mentioned. The only thing close I could find that was close was the free energy landscape using g_anaeig under the Dihedral PCA (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca) however, I'm not sure this is what I'm looking for. Does anyone know where I would be able to find out / read more about how to create potential energy landscapes from my simulation outputs? Thanks Natalie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: FEP
Hello Michael or others, It seems I'm still getting errors when doing a FEP on a molecule (a -CH3 to a -H). This below is for when I was charging things from a -H uncharged to -H charged, although it also happens when I'm actually converting the -CH3 to -H (at Lambdas greater than 85%). I made sure to keep the charges balanced at 0 while mutating and I did it at 3 steps like Michael Shirts suggested. Set 1: turn R-CH3 charges off in a way that preserves the total charge. Set 2: change CH3 LJ to H LJ Set 3: Turn R-H charges on in a way that preserves the total charge. In the portion of the error below atom 9 is -C9-(H67,H68,H66) which in this specific case H67 is already a dummy molecule with no mass or charge. From what I can see, it seems that the atoms do not know how to treat the dummy molecules in terms of angles. How should I treat the dummy molecules? Should I be treating them like hollow spheres with no charge so I would assign them angle constraints? I think it can also be that I'm peturbing the dihedral angles incorrectly. I received errors at first saying that dihedral multiplicities can't be peturbed so I had to equal the multiplicities just to get it to run. Does anybody have any experience with this? Thank you for your help. -Fabian Casteblanco Portion of Error Output: - Reading file nvt0.5.tpr, VERSION 4.5.3 (single precision) starting mdrun 'SIMVASTATIN' 15 steps,300.0 ps. Step 7, time 0.014 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.006111, max 0.139443 (between atoms 9 and 67) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007341, max 0.167622 (between atoms 9 and 67) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.008771, max 0.201182 (between atoms 9 and 67) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hi all, I have an additional question related to what Steven Neumann was mentioning. I actually have to do a molecule mutation. I'm trying to use Michael Shirts method 1) making small changes 'alchemical' changes in the molecules and computing the free energies by any method (BAR, TI, etc). I'm specifically want to try to use BAR at the end once I collect all the data. This helped a lot on clarification since it seemed that Justin's tutorial is essentially a FEP except its using the BAR mathematical method for computing the complete decoupling of the molecule rather than using the old FEP mathematics of the exponential averaging formula. So BAR is only referring to the mathematical code used to calculate the overall free energy for the FEP, correct? My question is, for a mutation of a -CH3 group to a -H group, is it better to simply run: [+ from (Lambda=0 , R-CH3, full charges and interactions -STATE A) -- (Lambda=1, R-CH, full charges and interactions -STATE B)] OR [1) from (Lambda=0 , R-CH3, STATE A : Charges and LJ Interactions: ON) 2) (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated) 3) (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF) 4) (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and Mutated to -H) 5) (Lambda=1, R-CH3, -CH3 STATE B : Charges and LJ Interactions: ON) Reason I'm asking is because when I try the first choice to do it STATE A to STATE B in one step, when I reach Lambda=0.85 and above on the NVT equilibration right after EM, I receive errors saying that bonds are moving way to far off their constraints which leads me to believe that the system is moving too far from where it was energy minimized. Errors such as: Step 188, time 0.376 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.17, max 0.000636 (between atoms 9 and 68) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 9 68 31.2 0. 0.1110 0. Step 188, time 0.376 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.15, max 0.000531 (between atoms 9 and 68) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 9 68 31.0 0. 0.1110 0. **Please, if anybody can help, I would greatly appreciate it. Thanks. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering C: +908 917 0723 E: fabian.castebla...@gmail.com -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E:
Re: [gmx-users] Uniform Distribution of drug molecules inside water spc216
meisam valizadeh kiamahalleh wrote: Dear GMX users Good day to you I have some drug molecules (cisplatin) added manually and randomly inside a system which is going to be solvated in spc216 water. I used genbox command to add the correct number of water molecules needed to solvate the box. The drug molecules are located very closed to each other. Kindly, would you please let me know how I can distribute drug molecules uniformly among the water molecoules to obtain a certain concentration of the drug? May I know if there is any specific tool or script which can help me to do it? I don't know how you did the initial insertion, but genbox -ci -nmol will add molecules randomly, after which you can solvate with water. Don't combine these steps. Do the insertion, then add the water. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?
From the Gromacs on GPU page (http://www.gromacs.org/Downloads/Installation_Instructions/GPUs) These are the compatible GPU cards (Basically buy NVidia for now): v2.0 Compatible NVIDIA CUDA versions (also see OpenMM version compatibility above): v3.x Compatible hardware (for details consult the NVIDIA CUDA GPUs list): G92/G94: GeForce 9800 GX2/GTX/GTX+/GT GeForce 9800M GT GeForce GTS 150, 250 GeForce GTX 280M, 285M Quadro FX 4700 Quadro Plex 2100 D4 GT200: GeForce GTX 260, 270, 280, 285, 295 Tesla C1060, S1070, M1060 Quadro FX 4800, 5800 Quadro CX Quadro Plex 2200 D2, 2200 S4 GF1xx (Fermi) GeForce GTX 460, 465, 470, 480, 570, 580 Tesla C2050, C2070, M2050, M2070 --- I got an EVGA Geforce GTX 580, which is about $450 for trying out GPU based MD, and has 512 GPU cores and a high clock rate, 1.5 gigs of memory. Having more cores and more memory are both important things for the GPU side of molecular dynamics (cores = more parallel, memory = more atoms and less memory transferring). I think you have some limitations with the GPU sims, like atoms 100,000. It is amazing that with implicit solvent you can really see a huge benefit and perhaps that might open some new doors. -Matt Larson On Wed, Oct 12, 2011 at 9:54 AM, Szilárd Páll szilard.p...@cbr.su.se wrote: Dear Stephan, Radeons work as well. You can put a 3-4 GPU board together with the highest end AMD or Intel chip for 3K, plus 16G RAM if you look around for a day or two, but the cooling is the main problem (with 1/4 the price radeons Vs. GTI cards), so one has to take cooling into account (h20 cost another 800$, or investing in 4-6 good fans/cooling an additional 2-300$). If you have a slightly higher budget you can get multi CPU boards with 4 GPU slots, ie 4 or 8 CPU's (direct via mail from Taiwan), but the CPU's and GPU's is where the money is spent. No, Radeons don't work and won't work in the near future - Gromacs doesn't support OpenCL. Cooling needs attention, but in reality it's nowhere near $2-300 extra - unless you want the fans with funky leds. Btw, what software is the above hardware description targeting? To me it sounds more like a gaming rig and not something specifically aiming at maximum performance with Gromacs 4.5 (nor 4.6 which is yet to be released). As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon 5900 series (double percission, single is supposed to run around 4 tera flops per GPU, so depends on your needs, desires as far as simulations), and the latest Intel 970's are around 400-500 Gflops/chip. Again, I might be missing something, but how exactly does Gromacs run on Radeons? I assume when referring to the i7 970 (?) above you meant 40-50 GFlops/chip - the i7 970 should have 70 GFlops peak. Also note that Flops are not every useful, what matters is time to solution for the specific problem one wants to solve. Cheers, -- Szilárd -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] protein-water distance restraints
Dear Gromacs-users,I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation.I though that I could implement intermolecular distance restraints between a water residue an the protein, but I did not manage that and all the suggestions I found here to implement intermolecular distance restraints seem not to work out for water - protein contacts. Does anybody has a suggestion how to implement such restraints ? Would the pull-code an option for my problem ?Thank you very muchMarkusSMS schreiben mit WEB.DE FreeMail - einfach, schnell undkostenguenstig. Jetzt gleich testen! http://f.web.de/?mc=021192 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] protein-water distance restraints
Dear Markus, If you know the residues composing the cavity (and I think you know it), you can simply change the coordinates of the water molecule in the .gro file to move the water in the cavity. Francesco Il 12/10/2011 18:17, Markus Weingarth ha scritto: Dear Gromacs-users, I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation. I though that I could implement intermolecular distance restraints between a water residue an the protein, but I did not manage that and all the suggestions I found here to implement intermolecular distance restraints seem not to work out for water - protein contacts. Does anybody has a suggestion how to implement such restraints ? Would the pull-code an option for my problem ? Thank you very much Markus SMS schreiben mit WEB.DE FreeMail - einfach, schnell und kostenguenstig. Jetzt gleich testen! *http://f.web.de/?mc=021192* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] protein-water distance restraints
Hi Francesco,Thanks for your answer, but that's not an option for me. I really would like to force the penetreation of a water-molecule into this cavity over the couse of the trajectory.CheersMarkusVon: Francesco Oteri francesco.ot...@gmail.comGesendet: Oct 12, 2011 6:41:05 PMAn: gmx-users@gromacs.orgBetreff: Re: [gmx-users] protein-water distance restraintsDear Markus,If you know the residues composing the cavity (and I think you know it), you can simply change the coordinatesof the water molecule in the .gro file to move the water in the cavity.FrancescoIl 12/10/2011 18:17, Markus Weingarth ha scritto:Dear Gromacs-users,I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation.I though that I could implement intermolecular distance restraints between a water residue an the protein, but I did not manage that and all the suggestions I found here to implement intermolecular distance restraints seem not to work out for water - protein contacts. Does anybody has a suggestion how to implement such restraints ? Would the pull-code an option for my problem ?Thank you very muchMarkusSMS schreiben mit WEB.DE FreeMail - einfach, schnell undkostenguenstig. Jetzt gleich testen! http://f.web.de/?mc=021192 SMS schreiben mit WEB.DE FreeMail - einfach, schnell undkostenguenstig. Jetzt gleich testen! http://f.web.de/?mc=021192 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] protein-water distance restraints
Markus Weingarth wrote: Hi Francesco, Thanks for your answer, but that's not an option for me. I really would like to force the penetreation of a water-molecule into this cavity over the couse of the trajectory. Use the pull code. -Justin Cheers Markus *Von:* Francesco Oteri francesco.ot...@gmail.com *Gesendet:* Oct 12, 2011 6:41:05 PM *An:* gmx-users@gromacs.org *Betreff:* Re: [gmx-users] protein-water distance restraints Dear Markus, If you know the residues composing the cavity (and I think you know it), you can simply change the coordinates of the water molecule in the .gro file to move the water in the cavity. Francesco Il 12/10/2011 18:17, Markus Weingarth ha scritto: Dear Gromacs-users, I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation. I though that I could implement intermolecular distance restraints between a water residue an the protein, but I did not manage that and all the suggestions I found here to implement intermolecular distance restraints seem not to work out for water - protein contacts. Does anybody has a suggestion how to implement such restraints ? Would the pull-code an option for my problem ? Thank you very much Markus SMS schreiben mit WEB.DE FreeMail - einfach, schnell und kostenguenstig. Jetzt gleich testen! *http://f.web.de/?mc=021192* https://freemailng0502.web.de/jump.htm?goto=http%3A%2F%2Ff.web.de%2F%3Fmc%3D021192 SMS schreiben mit WEB.DE FreeMail - einfach, schnell und kostenguenstig. Jetzt gleich testen! *http://f.web.de/?mc=021192* -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Potential Energy Landscape
Natalie Stephenson wrote: I was recently told in passing that it would be possible to construct a 'potential energy landscape' from the simulations I have performed. This way I could remove any loading rate differences between simulations and experimental force experiments I've been performing ... however I cannot find anywhere in which this is mentioned. The only thing close I could find that was close was the free energy landscape using g_anaeig under the Dihedral PCA (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca) however, I'm not sure this is what I'm looking for. Does anyone know where I would be able to find out / read more about how to create potential energy landscapes from my simulation outputs? g_sham produces free energy landscapes for any variables plotted against one another. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] mktop
Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging the output of mktop into gromacs MD simulation. Thanks, Pramod -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] mktop
ram bio wrote: Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging the output of mktop into gromacs MD simulation. You can #include any molecule topology in a system .top, provided you have the right format: http://www.gromacs.org/Documentation/File_Formats/.itp_File There is no tutorial for using mktop with a protein-ligand/membrane system, but there are tutorials for protein-ligand complexes: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html and membrane protein systems: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Fwd: [gmx-users] mktop
Dear Justin, Thanks for the information. Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file generated from the pdb2gmx. During the pdb2gmx command, i used opls FF. The coordinates of ligand used as input for mktop were added to the output of pdb2gmx (process.pdb - only protein coordinates), so that the structure file along with ligand coordinates (processlig.pdb) can be used for further steps. I doubt whether the procedure followed by me is correct, as when i execute grompp command to add ions i am getting errors : grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr ERROR 1 [file ligand.itp, line 291]: No default Ryckaert-Bell. types .. --- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1526 Fatal error: [ file ligand.itp, line 397 ]: Atom index (0) in dihedrals out of bounds (1-53). This probably means that you have inserted topology section dihedrals in a part belonging to a different molecule than you intended to. In that case move the dihedrals section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The commands executed to reach the grompp step are as follows: pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb editconf -f processlig.pdb -o procent.pdb -princ editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr I have attached the topol.top, ligand.itp files for your information, Please let me know your suggestions to fix this error. Thanks, Pramod On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging the output of mktop into gromacs MD simulation. You can #include any molecule topology in a system .top, provided you have the right format: http://www.gromacs.org/**Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File There is no tutorial for using mktop with a protein-ligand/membrane system, but there are tutorials for protein-ligand complexes: http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** gmx-tutorials/complex/index.**htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html and membrane protein systems: http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** gmx-tutorials/membrane_**protein/index.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists ligand.itp Description: Binary data topol.top Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 90, Issue 48
Dear Justin Thank you very much for your always prompt reply. Actually, I added many of drug molecules by copying and pasting a single molecule in discovery studio software. I could even move the drug molecules to any desired locations by select and dragging them. Finally I used the output pdb file from discovery studio as initial structure in Gromacs, but I could not find any option for the molecule uniform distribution. 1) May I know if I should use the drug resname or molecule name infront of -nmol? 2) As you mention the method suggested by you would add the drug molecules randomly. then, May I also Know if they can be uniformly distributed in the water after solvation? Thank you very much Best regards Meisam meisam valizadeh kiamahalleh wrote: Dear GMX users Good day to you I have some drug molecules (cisplatin) added manually and randomly inside a system which is going to be solvated in spc216 water. I used genbox command to add the correct number of water molecules needed to solvate the box. The drug molecules are located very closed to each other. Kindly, would you please let me know how I can distribute drug molecules uniformly among the water molecoules to obtain a certain concentration of the drug? May I know if there is any specific tool or script which can help me to do it? I don't know how you did the initial insertion, but genbox -ci -nmol will add molecules randomly, after which you can solvate with water. Don't combine these steps. Do the insertion, then add the water. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] mktop
ram bio wrote: Dear Justin, Thanks for the information. Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file generated from the pdb2gmx. During the pdb2gmx command, i used opls FF. The coordinates of ligand used as input for mktop were added to the output of pdb2gmx (process.pdb - only protein coordinates), so that the structure file along with ligand coordinates (processlig.pdb) can be used for further steps. I doubt whether the procedure followed by me is correct, as when i execute grompp command to add ions i am getting errors : grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr ERROR 1 [file ligand.itp, line 291]: No default Ryckaert-Bell. types .. --- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1526 Fatal error: [ file ligand.itp, line 397 ]: Atom index (0) in dihedrals out of bounds (1-53). This probably means that you have inserted topology section dihedrals in a part belonging to a different molecule than you intended to. In that case move the dihedrals section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The commands executed to reach the grompp step are as follows: pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb editconf -f processlig.pdb -o procent.pdb -princ editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr I have attached the topol.top, ligand.itp and procentsolv.gro files for your information, Please let me know your suggestions to fix this error. The ligand.itp file is trash. Most of your atoms have zero charge (except for a few that have +/- 1...yikes!) and on line 397 (as cited in the error message) atom 0 is referenced, which of course does not exist, since numbering starts with 1. You also have some exotic atom types present, and thus bonded parameters cannot be assigned, as grompp complained earlier. You need a better quality topology, and perhaps a different force field that might be suited for doing these simulations. -Justin Thanks, Pramod On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging the output of mktop into gromacs MD simulation. You can #include any molecule topology in a system .top, provided you have the right format: http://www.gromacs.org/__Documentation/File_Formats/.__itp_File http://www.gromacs.org/Documentation/File_Formats/.itp_File There is no tutorial for using mktop with a protein-ligand/membrane system, but there are tutorials for protein-ligand complexes: http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html and membrane protein systems: http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Uniform Distribution of drug molecules inside water spc216
meisam valizadeh kiamahalleh wrote: Dear Justin Thank you very much for your always prompt reply. Actually, I added many of drug molecules by copying and pasting a single molecule in discovery studio software. I could even move the drug molecules to any desired locations by select and dragging them. Finally I used the output pdb file from discovery studio as initial structure in Gromacs, but I could not find any option for the molecule uniform distribution. 1) May I know if I should use the drug resname or molecule name infront of -nmol? The -nmol option takes an integer argument. Please see genbox -h. 2) As you mention the method suggested by you would add the drug molecules randomly. then, May I also Know if they can be uniformly distributed in the water after solvation? You can only build a random configuration with genbox -ci -nmol. If you want an artificially crystalline system, use genconf -nbox to replicate your existing drug molecule as many times as you'd like in whatever dimensions you want. Either way, you'll have to do sufficient equilibration to get a homogeneous system, if it's even possible. I'd think the latter approach would be worse since you're starting from a very highly ordered system. -Justin Thank you very much Best regards Meisam meisam valizadeh kiamahalleh wrote: Dear GMX users Good day to you I have some drug molecules (cisplatin) added manually and randomly inside a system which is going to be solvated in spc216 water. I used genbox command to add the correct number of water molecules needed to solvate the box. The drug molecules are located very closed to each other. Kindly, would you please let me know how I can distribute drug molecules uniformly among the water molecoules to obtain a certain concentration of the drug? May I know if there is any specific tool or script which can help me to do it? I don't know how you did the initial insertion, but genbox -ci -nmol will add molecules randomly, after which you can solvate with water. Don't combine these steps. Do the insertion, then add the water. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] mktop
Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules. I have also tried swiss param to generate the ligand parameters to be used in protein ligand simulation using gromacs. The force field i am using for simulations is OPLS. My ligand contains an azido group and a tropane ring with protonated nitrogen. SwissParam force field has been designed to be compatible with the Charmm force field, but they are not tested on opls.Using the ligand topologies from swissparam, i was able to run the MD simulations using gromacs with opls without errors (swissparam - gromacs tutorial), only issues being the charges on the ligand, so i generated various input files (mol2 files) for swissparam with charges generated using ambcc1, gastergier and MMFF. But the itp files obtained from swissparam had same charges for the ligand atoms irrespective of the input provided i.e. charged or uncharged mol2 files, and As per Gromacs website: Note that an .itp filehttp://www.gromacs.org/Documentation/File_Formats/.itp_Filewill be specific to a given force field, and will only function when included by a .top filehttp://www.gromacs.org/Documentation/File_Formats/.top_Filethat has previously included the .itp files http://www.gromacs.org/Documentation/File_Formats/.itp_File for that force field. Appropriate use of the #define and #ifdef mechanisms can permit the same .itp filehttp://www.gromacs.org/Documentation/File_Formats/.itp_Fileto work with multiple force fields, e.g. share/top/water.itp. so, i think even though the swissparam generated topologies based on MMFF fit to charmm (based on testing), they could also be used with opls. It was informed by swiss param team that the ligand parameters generated by swissparam could also be used with opls FF in principle as they are based on MMFF So, in order to cross check or validate my results i was trying to use mktop to generate the ligand topologies for MD simulations. Please let me know your comments and suggestions on the procedure , regarding the compatibility of MMFF generated topologies to be used by OPLS and other methods to validate my results. Thanks, Pramod On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the information. Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file generated from the pdb2gmx. During the pdb2gmx command, i used opls FF. The coordinates of ligand used as input for mktop were added to the output of pdb2gmx (process.pdb - only protein coordinates), so that the structure file along with ligand coordinates (processlig.pdb) can be used for further steps. I doubt whether the procedure followed by me is correct, as when i execute grompp command to add ions i am getting errors : grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr ERROR 1 [file ligand.itp, line 291]: No default Ryckaert-Bell. types .. --**- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1526 Fatal error: [ file ligand.itp, line 397 ]: Atom index (0) in dihedrals out of bounds (1-53). This probably means that you have inserted topology section dihedrals in a part belonging to a different molecule than you intended to. In that case move the dihedrals section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- The commands executed to reach the grompp step are as follows: pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb editconf -f processlig.pdb -o procent.pdb -princ editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr I have attached the topol.top, ligand.itp and procentsolv.gro files for your information, Please let me know your suggestions to fix this error. The ligand.itp file is trash. Most of your atoms have zero charge (except for a few that have +/- 1...yikes!) and on line 397 (as cited in the error message) atom 0 is referenced, which of course does not exist, since numbering starts with 1. You also have some exotic atom types present, and thus bonded parameters cannot be assigned, as grompp complained earlier. You need a better quality topology, and perhaps a different force field that might be suited for doing these simulations. -Justin Thanks,
Re: [gmx-users] mktop
ram bio wrote: Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules. I understand that. The program did a poor job, per the reasons I cited before. I do not know anything about mktop (other than what it does), so I cannot analyze its suitability here, but due to missing parameters and bogus charges, you should not use that topology for anything. I have also tried swiss param to generate the ligand parameters to be used in protein ligand simulation using gromacs. The force field i am using for simulations is OPLS. My ligand contains an azido group and a tropane ring with protonated nitrogen. SwissParam force field has been designed to be compatible with the Charmm force field, but they are not tested on opls.Using the ligand topologies from swissparam, i was able to run the MD simulations using gromacs with opls without errors (swissparam - gromacs tutorial), only issues being the charges on the ligand, so i generated various input files (mol2 files) for swissparam with charges generated using ambcc1, gastergier and MMFF. But the itp files obtained from swissparam had same charges for the ligand atoms irrespective of the input provided i.e. charged or uncharged mol2 files, and If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not? I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). As per Gromacs website: Note that an .itp file http://www.gromacs.org/Documentation/File_Formats/.itp_File will be specific to a given force field, and will only function when included by a .top file http://www.gromacs.org/Documentation/File_Formats/.top_File that has previously included the .itp files http://www.gromacs.org/Documentation/File_Formats/.itp_File for that force field. Appropriate use of the |#define| and |#ifdef| mechanisms can permit the same .itp file http://www.gromacs.org/Documentation/File_Formats/.itp_File to work with multiple force fields, e.g. |share/top/water.itp|. Note the key caveat here - through the use of #define and #ifdef you can make use of different force fields. That means you can control which parameters are applied based on different conditions. I could write an .itp file for any molecule that has force field parameters for any force field, and all I'd have to do is enclose all relevant directives within #ifdef blocks and it would work. This note does *not* indicate that you can mix and match force fields. Doing so is generally a very bad idea, if it even works syntactically. so, i think even though the swissparam generated topologies based on MMFF fit to charmm (based on testing), they could also be used with opls. It was informed by swiss param team that the ligand parameters generated by swissparam could also be used with opls FF in principle as they are based on MMFF So, in order to cross check or validate my results i was trying to use mktop to generate the ligand topologies for MD simulations. Maybe the SwissParam-generated topology will work. There are commonalities underlying these force fields, to be sure. Still, the methodology for properly deriving OPLS parameters is quite well described in the literature, right down to the QM basis sets required to run the geometry optimizations and charge calculations. -Justin Please let me know your comments and suggestions on the procedure , regarding the compatibility of MMFF generated topologies to be used by OPLS and other methods to validate my results. Thanks, Pramod On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the information. Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file generated from the pdb2gmx. During the pdb2gmx command, i used opls FF. The coordinates of ligand used as input for mktop were added to the output of pdb2gmx (process.pdb - only protein coordinates), so that the structure file along with ligand coordinates (processlig.pdb) can be used for further steps. I doubt whether the procedure followed by me is correct, as when i execute grompp command to add ions i am getting errors : grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr ERROR 1 [file ligand.itp, line 291]: No default
[gmx-users] Peturbing a Dihedral for FEP
Hello all, It seems I'm still getting errors when doing a FEP on a molecule (a -CH3 to a -H). This below is for when I was charging things from a -H uncharged to -H charged, although it also happens when I'm actually converting the -CH3 to -H (at Lambdas greater than 85%). I made sure to keep the charges balanced at 0 while mutating and I did it at 3 steps like Michael Shirts suggested. Set 1: turn R-CH3 charges off in a way that preserves the total charge. Set 2: change CH3 LJ to H LJ Set 3: Turn R-H charges on in a way that preserves the total charge. In the portion of the error below atom 9 is -C9-(H67,H68,H66) which in this specific case H67 is already a dummy molecule with no mass or charge. From what I can see, it seems that the atoms do not know how to treat the dummy molecules in terms of angles. How should I treat the dummy molecules? Should I be treating them like hollow spheres with no charge so I would assign them angle constraints? I think it can also be that I'm peturbing the dihedral angles incorrectly. I received errors at first saying that dihedral multiplicities can't be peturbed so I had to equal the multiplicities just to get it to run. Does anybody have any experience with this? Thank you for your help. -Fabian Casteblanco Portion of Error Output: - Reading file nvt0.5.tpr, VERSION 4.5.3 (single precision) starting mdrun 'SIMVASTATIN' 15 steps, 300.0 ps. Step 7, time 0.014 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.006111, max 0.139443 (between atoms 9 and 67) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007341, max 0.167622 (between atoms 9 and 67) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.008771, max 0.201182 (between atoms 9 and 67) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hi all, I have an additional question related to what Steven Neumann was mentioning. I actually have to do a molecule mutation. I'm trying to use Michael Shirts method 1) making small changes 'alchemical' changes in the molecules and computing the free energies by any method (BAR, TI, etc). I'm specifically want to try to use BAR at the end once I collect all the data. This helped a lot on clarification since it seemed that Justin's tutorial is essentially a FEP except its using the BAR mathematical method for computing the complete decoupling of the molecule rather than using the old FEP mathematics of the exponential averaging formula. So BAR is only referring to the mathematical code used to calculate the overall free energy for the FEP, correct? My question is, for a mutation of a -CH3 group to a -H group, is it better to simply run: [+ from (Lambda=0 , R-CH3, full charges and interactions -STATE A) -- (Lambda=1, R-CH, full charges and interactions -STATE B)] OR [1) from (Lambda=0 , R-CH3, STATE A : Charges and LJ Interactions: ON) 2) (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated) 3) (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF) 4) (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and Mutated to -H) 5) (Lambda=1, R-CH3, -CH3 STATE B : Charges and LJ Interactions: ON) Reason I'm asking is because when I try the first choice to do it STATE A to STATE B in one step, when I reach Lambda=0.85 and above on the NVT equilibration right after EM, I receive errors saying that bonds are moving way to far off their constraints which leads me to believe that the system is moving too far from where it was energy minimized. Errors such as: Step 188, time 0.376 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.17, max 0.000636 (between atoms 9 and 68) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 9 68 31.2 0. 0.1110 0. Step 188, time 0.376 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.15, max 0.000531 (between atoms 9 and 68) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 9 68 31.0 0. 0.1110 0. **Please, if anybody can help, I would greatly appreciate it. Thanks. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering C: +908 917 0723 E: fabian.castebla...@gmail.com -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917
Re: [gmx-users] mktop
Dear Justin, Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). Yes, I also tried CHARMM FF to generate the topology file of the protein using pdb2gmx (without ligand), and as per the swissparam and gromacs tutorial i could build the protein-ligand-lipid bilayer and minimize it using mdrun and and i am at the NPT equilibration step, everything is ok with this procedure and without errors, but my lipid bilayer is made up of POPC and the POPC itp file has OPLS FF topologies. So, i was wondering whether the POPC itp file i am using for MD simulations can be used with the protein and ligand topology file generated by CHARMM. and as per the swissparam tutorial the command to generate topology file for protein is: pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx command is available, but i could not understand the usage of -nochargegp flag as per the tutorial, is this flag still valid while generating toplogies. Please let me know your comments and suggestions regarding the procedure followed and the itp files usage for gromacs MD simulations. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules. I understand that. The program did a poor job, per the reasons I cited before. I do not know anything about mktop (other than what it does), so I cannot analyze its suitability here, but due to missing parameters and bogus charges, you should not use that topology for anything. I have also tried swiss param to generate the ligand parameters to be used in protein ligand simulation using gromacs. The force field i am using for simulations is OPLS. My ligand contains an azido group and a tropane ring with protonated nitrogen. SwissParam force field has been designed to be compatible with the Charmm force field, but they are not tested on opls.Using the ligand topologies from swissparam, i was able to run the MD simulations using gromacs with opls without errors (swissparam - gromacs tutorial), only issues being the charges on the ligand, so i generated various input files (mol2 files) for swissparam with charges generated using ambcc1, gastergier and MMFF. But the itp files obtained from swissparam had same charges for the ligand atoms irrespective of the input provided i.e. charged or uncharged mol2 files, and If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not? I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). As per Gromacs website: Note that an .itp file http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File will be specific to a given force field, and will only function when included by a .top file http://www.gromacs.org/** Documentation/File_Formats/.**top_Filehttp://www.gromacs.org/Documentation/File_Formats/.top_File that has previously included the .itp files http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File for that force field. Appropriate use of the |#define| and |#ifdef| mechanisms can permit the same .itp file http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File to work with multiple force fields, e.g. |share/top/water.itp|. Note the key caveat here - through the use of #define and #ifdef you can make use of different force fields. That means you can control which parameters are applied based on different conditions. I could write an .itp file for any molecule that has force field parameters for any force field, and all I'd have to do is enclose all relevant directives within #ifdef blocks and it would work. This note does *not* indicate that you can mix and match force fields. Doing so is generally a very bad idea, if it even works syntactically. so, i think even though the swissparam generated topologies based on MMFF fit to charmm (based on testing), they could also be used with opls. It was
Re: [gmx-users] mktop/swissparam
Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). Yes, I also tried CHARMM FF to generate the topology file of the protein using pdb2gmx (without ligand), and as per the swissparam and gromacs tutorial i could build the protein-ligand-lipid bilayer and minimize it using mdrun and and i am at the NPT equilibration step, everything is ok with this procedure and without errors, but my lipid bilayer is made up of POPC and the POPC itp file has OPLS FF topologies. So, i was wondering whether the POPC itp file i am using for MD simulations can be used with the protein and ligand topology file generated by CHARMM. and as per the swissparam tutorial the command to generate topology file for protein is: pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx command is available, but i could not understand the usage of -nochargegp flag as per the tutorial, is this flag still valid while generating toplogies. Please let me know your comments and suggestions regarding the procedure followed and the itp files usage for gromacs MD simulations. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules. I understand that. The program did a poor job, per the reasons I cited before. I do not know anything about mktop (other than what it does), so I cannot analyze its suitability here, but due to missing parameters and bogus charges, you should not use that topology for anything. I have also tried swiss param to generate the ligand parameters to be used in protein ligand simulation using gromacs. The force field i am using for simulations is OPLS. My ligand contains an azido group and a tropane ring with protonated nitrogen. SwissParam force field has been designed to be compatible with the Charmm force field, but they are not tested on opls.Using the ligand topologies from swissparam, i was able to run the MD simulations using gromacs with opls without errors (swissparam - gromacs tutorial), only issues being the charges on the ligand, so i generated various input files (mol2 files) for swissparam with charges generated using ambcc1, gastergier and MMFF. But the itp files obtained from swissparam had same charges for the ligand atoms irrespective of the input provided i.e. charged or uncharged mol2 files, and If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not? I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). As per Gromacs website: Note that an .itp file http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File will be specific to a given force field, and will only function when included by a .top file http://www.gromacs.org/** Documentation/File_Formats/.**top_Filehttp://www.gromacs.org/Documentation/File_Formats/.top_File that has previously included the .itp files http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File for that force field. Appropriate use of the |#define| and |#ifdef| mechanisms can permit the same .itp file http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File to work with multiple force fields, e.g. |share/top/water.itp|. Note the key caveat here - through the use of #define and #ifdef you can make use of different force fields. That means you can control which parameters are applied based on different conditions. I could write an .itp file for any molecule that has force field parameters for any force field, and all I'd have to do is enclose all relevant directives within #ifdef blocks and it would work. This note does *not* indicate that you can mix and match force fields. Doing so is generally a very bad idea, if it even works syntactically. so, i think even though the swissparam generated topologies based on MMFF fit to charmm (based on testing), they could also be used
RE: [gmx-users] Implicit solvent problems
Did you look at atom 2073? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - 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 liaoxyi Sent: Wednesday, 12 October 2011 3:59 PM To: gmx-users@gromacs.org Subject: [gmx-users] Implicit solvent problems Hi, dear all, I'm doing the simulation involved in protein and some surface. I encounter this problem when trying to use implicit solvent model with GMX4.5.3. First, minimize. When doing this I got the result as below: Step=0, Dmax= 1.0e-02 nm, Epot= -1.91727e+06 Fmax= 6.19542e+06, atom= 2073 Step=1, Dmax= 1.0e-02 nm, Epot= -1.99260e+06 Fmax= 1.05712e+06, atom= 2073 Step=2, Dmax= 1.2e-02 nm, Epot= -2.09734e+06 Fmax= 1.79058e+05, atom= 2073 Step=4, Dmax= 7.2e-03 nm, Epot= -2.17474e+06 Fmax= 7.22113e+04, atom= 2073 Step=6, Dmax= 4.3e-03 nm, Epot= -2.17724e+06 Fmax= 4.33926e+04, atom= 2073 Step=8, Dmax= 2.6e-03 nm, Epot= -2.18069e+06 Fmax= 3.24778e+04, atom= 2073 Step= 10, Dmax= 1.6e-03 nm, Epot= -2.18404e+06 Fmax= 2.76114e+04, atom= 2073 Step= 13, Dmax= 4.7e-04 nm, Epot= -2.18500e+06 Fmax= 2.63803e+04, atom= 2073 Step= 17, Dmax= 7.0e-05 nm, Epot= -2.18514e+06 Fmax= 2.62045e+04, atom= 2073 Step= 19, Dmax= 4.2e-05 nm, Epot= -2.18522e+06 Fmax= 2.61000e+04, atom= 2073 Step= 22, Dmax= 1.3e-05 nm, Epot= -2.18524e+06 Fmax= 2.60689e+04, atom= 2073 Step= 23, Dmax= 1.5e-05 nm, Epot= -2.18527e+06 Fmax= 2.60315e+04, atom= 2073 Step= 27, Dmax= 2.3e-06 nm, Epot= -2.18527e+06 Fmax= 2.60258e+04, atom= 2073 Step= 29, Dmax= 1.4e-06 nm, Epot= -2.18488e+06 Fmax= 2.60222e+04, atom= 2073 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 30 steps, but did not reach the requested Fmax 1000. Potential Energy = -2.1852700e+06 Maximum force = 2.6025840e+04 on atom 2073 Norm of force = 2.2667976e+03 --- From above, the force is extremely large. And I don't know why. the minim.mdp is as below: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype = Cut-off ; for Implicit solvent long-range electrostatics rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) ; implicit_solvent implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1 rgbradii = 1.0 gb_epsilon_solvent = 78.3 gb_obc_alpha = 1 ; OBC(II) gb_obc_beta = 0.8 ; OBC(II) gb_obc_gamma = 4.85 ; OBC(II) gb_dielectric_offset = 0.09 - Is there any item that's not proper or needed to add? Is the minimization necessary for implicit solvent? Thank you again for your reading. Kiara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5
On 13/10/2011 12:35 AM, Nuno Azoia wrote: I know that from the beginning. That's why I found very strange the increasing on the system volume. My initial setup have a density of ~400g/L, and for liquid chloroform is ~1400g/L. Using gromacs-4.5 I get densities of about 200 after 750ps simulation time, and using 4.0 I get almost 500 after 1ns. Your chloroform parameters are probably only valid for a condensed phase, and your initial density is nowhere near that. Please follow the approach here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation. And I was using such low densities because I build the box using genconf with the options -nbox and -dist, starting with one molecule of chloroform. If I used small distance values I get LINCS warnings in the energy minimization step. Using genbox to solvate one empty box with chloroform, I get very strange behaviors, with a very large amount of molecule overlap. Shrug. Without command lines and descriptions of what is in your input, we are helpless. Please follow the above advice. But as you said before, I now think that this should be also a paralelization problem, not to mention the numerical instability caused by this very low density. And I think this is a paralelization problem associated with this numerical instability judging from the system behavior. In 4.5, using the option -nt in mdrun, I get some small droplets of liquid chloroform, and in 4.0, using mpi, I get one large droplet of chloroform. It looks like if 4.5 is treating the system like independent small systems, while 4.0 is able to divide the system into small, but interdependent systems. No, the implementation of parallelization might have an effect here if you were starting from a reasonable approximation of a condensed phase. These two observations are just two of the possible things that could happen to a liquid at extremely low density. Mark On Wed, Oct 12, 2011 at 12:26 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 12/10/2011 8:04 PM, Nuno Azoia wrote: Thank you Mark for your answer! I agree with you when you say that the high pressure is not itself a problem. To avoid that problem I change my system from 1000 molecules to 27000 molecules, and the pressure change from several thousands to several hundreds bar. What I found very strange was the increasing volume (and pressure). My system is very unstable, I know, because the density is very low, and not the opposite, so I was expecting to see the box getting smaller. Looking to the trajectory I can see a box almost empty (with empty I mean empty space, with chloroform molecules aggregating in small droplets), and that's why I found the system behavior very strange. Sounds like your initial density might be far too low. grompp reports it, so do check. Mark I will follow your suggestion concerning nsttcouple and nstpcouple and the other initial conditions. Nuno Azoia On Wed, Oct 12, 2011 at 6:24 AM, Mark Abrahammark.abra...@anu.edu.au wrote: On 12/10/2011 2:22 AM, Nuno Azoia wrote: Hello! I found something very strange while making a CHCl3 box using gromacs-4.5.5. A look the mailing list, the manual and some release notes for gromacs-4.5 and I couldn't found the answer for my problem. It's possible that I'm doing something wrong, but I can not find what, so I'm describe my problem. I start a chloroform box from scratch, using genconf, and I get o chloroform box with 1000 molecules. I get energy minimization without problems. Then I've run some equilibration steps in a NVT ensemble and in the end I get pressure in the order of hundreds of bar. The high pressure is not itself a problem - small numbers of molecules and short simulation times lead to doubtful statistics for pressure. Then I change to NPT conditions and both the pressure and the volume keep increasing with time. Be sure to visualize your trajectory to confirm its behaviour matches what you expect from the trends in P and V. To discard the possibility of a size problem, I repeat everything with a box of 27000 molecules, with a volume of ~13800 nm^3. The problem was the same. Very high pressures (150-200 bar) and very low densities ( 200 g/L) after 750 ps simulation time. And both volume and pressure increasing with time. I'm doing now the same procedure, but using gromacs-4.0.7 and I'm getting very different (and better) results. After energy minimization I run 5 steps in a nvt ensemble and I got pressure around -30 bar (Ok for me). After that I start to run the simulations in npt ensemble and the pressure start to increase slowly, with negative values because the system have very low densities (~400 g/L), and the volume is decreasing. So I'm getting the normal reaction from the system. Where is the problem? There are some different parameters to set in the mdp file and I didn't realize that, or is this a problem in gromacs-4.5? It seems you are generating some numerical instability with your choice
Re: [gmx-users] Uniform Distribution of drug molecules inside water spc216
On 13/10/2011 2:13 AM, meisam valizadeh kiamahalleh wrote: Dear GMX users Good day to you I have some drug molecules (cisplatin) added manually and randomly inside a system which is going to be solvated in spc216 water. I used genbox command to add the correct number of water molecules needed to solvate the box. The drug molecules are located very closed to each other. Kindly, would you please let me know how I can distribute drug molecules uniformly among the water molecoules to obtain a certain concentration of the drug? May I know if there is any specific tool or script which can help me to do it? Decide how many drug molecules you want in a box of a given size, and place one in a much smaller box. Then use genconf to replicate that small box up to the proper size. Use the genconf option to randomize the orientation, solvate with genbox, then equilibrate for a long time. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff
Done 2011/10/10 Mark Abraham mark.abra...@anu.edu.au On 11/10/2011 4:51 AM, César Ávila wrote: v4.5.4 As I commented above, I had to manually add an entrance for the cmap terms in the topology file as pdb2gmx would not generate them for the alanine dipeptide. There seems to be no problem for larger peptides. Cheers Cesar That sounds like a bug. Please describe your symptoms in a new issue here - http://redmine.gromacs.org Mark 2011/10/10 Jianguo Li ljg...@yahoo.com.sg which gromacs version are you using? cMAP is implemented in v4.5 or later Jianguo -- *From:* César Ávila clav...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Sunday, 9 October 2011 12:07 AM *Subject:* [gmx-users] CMAP for alanine dipeptide in Charmm27 ff I would like to run REMD simulations on the alanine dipeptide using the Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not see any entrance referring to the cmap term in the topology file. Does this mean that Cmap won't be calculated? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] mktop
ram bio wrote: Dear Justin, Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). Yes, I also tried CHARMM FF to generate the topology file of the protein using pdb2gmx (without ligand), and as per the swissparam and gromacs tutorial i could build the protein-ligand-lipid bilayer and minimize it using mdrun and and i am at the NPT equilibration step, everything is ok with this procedure and without errors, but my lipid bilayer is made up of POPC and the POPC itp file has OPLS FF topologies. So, i was wondering whether the POPC itp file i am using for MD simulations can be used with the protein and ligand topology file generated by CHARMM. You shouldn't mix and match force fields. Suitable CHARMM lipid parameters are widely available. and as per the swissparam tutorial the command to generate topology file for protein is: pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx command is available, but i could not understand the usage of -nochargegp flag as per the tutorial, is this flag still valid while generating toplogies. CHARMM does not use charge groups. Therefore, each atom should be its own group in the topology. Using -nochargegrp overrides the default behavior of the .rtp files (which has multi-atom charge groups, although I think this was changed somewhere along the way, but I don't remember if it was before or after 4.5.4). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?
G92/G94: GeForce 9800 GX2/GTX/GTX+/GT GeForce 9800M GT GeForce GTS 150, 250 GeForce GTX 280M, 285M Quadro FX 4700 Quadro Plex 2100 D4 GT200: GeForce GTX 260, 270, 280, 285, 295 Tesla C1060, S1070, M1060 Quadro FX 4800, 5800 Quadro CX Quadro Plex 2200 D2, 2200 S4 GF1xx (Fermi) GeForce GTX 460, 465, 470, 480, 570, 580 Tesla C2050, C2070, M2050, M2070 Ummm, that compatibility table is a little outdated. I've just added a few more cards (GTX 5xx, some 4xx, and Tesla 2090s, 2075s). I got an EVGA Geforce GTX 580, which is about $450 for trying out GPU based MD, and has 512 GPU cores and a high clock rate, 1.5 gigs of memory. Having more cores and more memory are both important things for the GPU side of molecular dynamics (cores = more parallel, memory = more atoms and less memory transferring). I think you have some limitations with the GPU sims, like atoms 100,000. It is amazing that with implicit solvent you can really see a huge benefit and perhaps that might open some new doors. Right, the GTX 580 is as fast as it gets. However, from a price/performance point of view the 570 way better and depending on the use case even a 560 can be a decent and cheap option. -- Szilárd On Wed, Oct 12, 2011 at 9:54 AM, Szilárd Páll szilard.p...@cbr.su.se wrote: Dear Stephan, Radeons work as well. You can put a 3-4 GPU board together with the highest end AMD or Intel chip for 3K, plus 16G RAM if you look around for a day or two, but the cooling is the main problem (with 1/4 the price radeons Vs. GTI cards), so one has to take cooling into account (h20 cost another 800$, or investing in 4-6 good fans/cooling an additional 2-300$). If you have a slightly higher budget you can get multi CPU boards with 4 GPU slots, ie 4 or 8 CPU's (direct via mail from Taiwan), but the CPU's and GPU's is where the money is spent. No, Radeons don't work and won't work in the near future - Gromacs doesn't support OpenCL. Cooling needs attention, but in reality it's nowhere near $2-300 extra - unless you want the fans with funky leds. Btw, what software is the above hardware description targeting? To me it sounds more like a gaming rig and not something specifically aiming at maximum performance with Gromacs 4.5 (nor 4.6 which is yet to be released). As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon 5900 series (double percission, single is supposed to run around 4 tera flops per GPU, so depends on your needs, desires as far as simulations), and the latest Intel 970's are around 400-500 Gflops/chip. Again, I might be missing something, but how exactly does Gromacs run on Radeons? I assume when referring to the i7 970 (?) above you meant 40-50 GFlops/chip - the i7 970 should have 70 GFlops peak. Also note that Flops are not every useful, what matters is time to solution for the specific problem one wants to solve. Cheers, -- Szilárd -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] mktop
Dear Justin, Thanks. The POPC bilayer i am using is with berger lipids, corrected for dihedrals so as to be compatible with the OPLS FF for aminoacids. While searching for the literature on compatibility of lipid FF and protein FF, I found few references where similar modification was done for DOPC lipid bilayer and were suitable with various FF for proteins and also with CHARMM FF: 1. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221–S1234 2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force Fields.J Comput Chem 32: 1400–1410, 2011. I don't have the lipid bilayer with their itp files with CHARMM FF parameterization. Please could you inform me where to obtain them, so that i can use the lipid bilayer structure for embedding the protein and use the related CHARMM FF parameterised itp in the topology file in gromacs for MD simulation. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). Yes, I also tried CHARMM FF to generate the topology file of the protein using pdb2gmx (without ligand), and as per the swissparam and gromacs tutorial i could build the protein-ligand-lipid bilayer and minimize it using mdrun and and i am at the NPT equilibration step, everything is ok with this procedure and without errors, but my lipid bilayer is made up of POPC and the POPC itp file has OPLS FF topologies. So, i was wondering whether the POPC itp file i am using for MD simulations can be used with the protein and ligand topology file generated by CHARMM. You shouldn't mix and match force fields. Suitable CHARMM lipid parameters are widely available. and as per the swissparam tutorial the command to generate topology file for protein is: pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx command is available, but i could not understand the usage of -nochargegp flag as per the tutorial, is this flag still valid while generating toplogies. CHARMM does not use charge groups. Therefore, each atom should be its own group in the topology. Using -nochargegrp overrides the default behavior of the .rtp files (which has multi-atom charge groups, although I think this was changed somewhere along the way, but I don't remember if it was before or after 4.5.4). -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] mktop
ram bio wrote: Dear Justin, Thanks. The POPC bilayer i am using is with berger lipids, corrected for dihedrals so as to be compatible with the OPLS FF for aminoacids. I think significantly more parameters than just dihedrals need to be altered to make the Berger united-atom force field compatible with OPLS. While searching for the literature on compatibility of lipid FF and protein FF, I found few references where similar modification was done for DOPC lipid bilayer and were suitable with various FF for proteins and also with CHARMM FF: 1. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221–S1234 2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force Fields.J Comput Chem 32: 1400–1410, 2011. I don't have the lipid bilayer with their itp files with CHARMM FF parameterization. Please could you inform me where to obtain them, so that i can use the lipid bilayer structure for embedding the protein and use the related CHARMM FF parameterised itp in the topology file in gromacs for MD simulation. The lipids are built into the CHARMM27 implementation in Gromacs. You can generate their topology with pdb2gmx. Run pdb2gmx on a single lipid, convert it to an .itp file, and #include it in the topology. The CHARMM36 force field is also available in the User Contributions section of the Gromacs website. -Justin Thanks in advance, Pramod On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). Yes, I also tried CHARMM FF to generate the topology file of the protein using pdb2gmx (without ligand), and as per the swissparam and gromacs tutorial i could build the protein-ligand-lipid bilayer and minimize it using mdrun and and i am at the NPT equilibration step, everything is ok with this procedure and without errors, but my lipid bilayer is made up of POPC and the POPC itp file has OPLS FF topologies. So, i was wondering whether the POPC itp file i am using for MD simulations can be used with the protein and ligand topology file generated by CHARMM. You shouldn't mix and match force fields. Suitable CHARMM lipid parameters are widely available. and as per the swissparam tutorial the command to generate topology file for protein is: pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx command is available, but i could not understand the usage of -nochargegp flag as per the tutorial, is this flag still valid while generating toplogies. CHARMM does not use charge groups. Therefore, each atom should be its own group in the topology. Using -nochargegrp overrides the default behavior of the .rtp files (which has multi-atom charge groups, although I think this was changed somewhere along the way, but I don't remember if it was before or after 4.5.4). -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
Re: [gmx-users] using gromacs with an specific GCC
Hi Nathalia, Right, gcc 4.1 is quite controversial as these is bug in it which is though to be causing mdrun crashes. So you better stay away from 4.1 as well as from other old gcc versions. I'd recommend 4.5 or 4.6 as these have gotten really good, even compared to icc - at least when it comes to Gromacs performance. I'd especially recommend 4.6 if you're using Nehalem CPUs (with the -mtune/-march=corei7 flag). Compiling gcc is rather straightforward and there are plenty of guide online. When it comes to running binaries, depending on where you install the new gcc you might have to set the LD_LIBRARY_PATH to contain the custom gcc installation's lib directory before the standard lib path. This is of course unless you link statically against standard libraries. Cheers, -- Szilárd On Mon, Oct 10, 2011 at 6:51 PM, Nathalia Garces natsgar...@gmail.com wrote: Good morning, I'm trying to use Scientific Linux 5.5 to run Gromacs 4.5.4. The problem is that the default version of gcc in this distribution is 4.1, which is broken for Gromacs!! I can install a newer version of gcc in compatible mode with gcc 4.1, but the last one will still be the default. Now, my problem is that I don't know how to specify to Gromacs to use the newer version. I've seen that you can specify which gcc to use while you configure the program, but I found no information of how to specify which compiler to use while running a MD simulation??.. I mean when using mdrun command or even while using every command in Gromacs. Thank you for four answer Nathalia -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
