[gmx-users] cluster fomation in triolein simulation
In God We Trust Hello Dear gmx-users I want to simulate oliver oil by Gromacs. I made topology of triolein with G45a3 force field at NPT ensemble (according to SCHULER paper ; Journal of Computational Chemistry, Vol. 22, No. 11, 1205–1218 (2001).I generated a box with 216 triolein molecules that had random orientation by genconf and used it as starting structure. After minimization and 50 ps MD simulation, system become coagulate and some clusters were formed, Is it normal for triolein?.What is my wrong?.Here is my mdp file: nvt.mdp: title = n.pdb warnings= 10 cpp = /lib/cpp constraints = none integrator = md dt = 0.001 nsteps = 5000 nstxout = 500 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy = 1000 nstcalcenergy = 10 nstlist = 5 ns_type = grid rlist = 0.8 coulombtype = PME vdw-type= shift rcoulomb= 0.8 rvdw= 1.4 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes energygrps = DRG ; check charge groups and energy groups! fourierspacing = 0.1 rlistlong = 1.6 ; Berendsen temperature coupling is on in three groups Tcoupl = V-rescale tau_t = 0.1 tc-grps = DRG ref_t = 300 ; Pressure coupling is on Pcoupl = no tau_p = 0.1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thank you very much for your help. Yours truly Karim Mahnam (PhD, Assistant Professor) Biology Dept., Faculty of Sciences, Shahrekod University, IRAN. Tel. 098-0381-4424407 Fax. 098-0381-4424419 -- 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] Tabulated potentials for dihedrals - regd
On 7/06/2012 4:33 AM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, According to my understanding functional form of dihedral function type 9 is same as dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except the difference that function type 9 is used to handle the multiple potential functions to be applied to the single dihedreal, Is my understanding correct ?. The functional form that I am using Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 is different from the k (1 + cos(n (phi)- phi s)). I am suspecting can I use function type 9 for my function. Can you please clarify my doubt. I said last time you can use type 9. You can use high-school maths to express your equation in the form of a sum of multiple type 1, which is type 9. The additive constant only affects the total energy, which is never used for the simulation. The derivative of V is used, so the constant goes away. Mark Thank you in advance. On Mon, Jun 4, 2012 at 12:55 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). You do not need a table for this - type 9 will do the job easily, and for friendly values of phi0, there exists an equivalent form to the above that can be expressed as a Ryckaert-Belleman dihedral. See various places of manual chapters 4 and 5. I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Your table would need to be the weighted sum of the three cosines, so apparently you have not yet generated such a table. But rather than buy trouble, go and do the easier and faster solutions above :-) Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- 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] GPU crashes
Did you play with the time step? Just currious, but I woundered what happened with 0.0008, 0.0005, 0.0002. I found if I had a good behaving protein, as soon as I added a small (non-protein) molecule which rotated wildly while attached to the protein, it would crash unless I reduced the time step to the above when constraints were removed after EQ ... always it seemed to me it didnt like the rotation or bond angles, seeing them as a violation but acted like it was an amino acid? (the same bond type but with wider rotation as one end wasnt fixed to a chain) If your loop moves via backbone, the calculated angles, bonds or whatever might appear to the computer to be violating the parameter settings for problems, errors, etc as it cant track them fast enough over the time step. Ie atom 1-2-3 and then delta 1-2-3 with xyz parameters, but then the particular set has additional rotation, etc and may include the chain atoms which bend wildly (n-Ca-Cb-Cg maybe a dihedral) but probab ly not this. Just a thought but probably not the right answere as well, it might be the way it is broken down (above) over GPUs, which convert everything to matricies (non-standard just for basic math operations not real matricies per say) for exicution and then some library problem which would not account for long range rapid (0.0005) movements at the chain (Ca,N,O to something else) and then tries to apply these to Cb-Cg-O-H, etc using the initial points while looking at the parameters for say a single amino acid...Maybe the constraints would cause this, which would make it a pain to EQ, but this allowed me to increase the time step, but would ruin the experiment I had worked on as I needed it unconstrained to show it didnt float away when proteins were pulled, etc...I was using a different integrator though...just normal MD. ANd your cutoffs for vdw, etc...Why are they 0? I dont know if this means a defautl set is then used...but if not ? Wouldnt they try integrating using both types of formula, or would it be just using coulumb or vice versa? (dont know what that would do to the code but assume it means no vdw, and all coulumb but then zeros are alwyas a problem for computers). Thats my thoughts on that. Probably something else though. Good luck, Stephan Original-Nachricht Datum: Wed, 06 Jun 2012 18:42:45 -0400 Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: [gmx-users] GPU crashes Hi All, I'm wondering if anyone has experienced what I'm seeing with Gromacs 4.5.5 on GPU. It seems that certain systems fail inexplicably. The system I am working with is a heterodimeric protein complex bound to DNA. After about 1 ns of simulation time using mdrun-gpu, all the energies become NaN. The simulations don't stop, they just carry on merrily producing nonsense. I would love to see some action regarding http://redmine.gromacs.org/issues/941 for this reason ;) I ran simulations of each of the components of the system individually - each protein alone, and DNA - to try to track down what might be causing this problem. The DNA simulation is perfectly stable out to 10 ns, but each protein fails within 2 ns. Each protein has two domains with a flexible linker, and it seems that as soon as the linker flexes a bit, the simulations go poof. Well-behaved proteins like lysozyme and DHFR (from the benchmark set) seem fine, but anything that twitches even a small amount fails. This is very unfortunate for us, as we are hoping to see domain motions on a feasible time scale using implicit solvent on GPU hardware. Has anyone seen anything like this? Our Gromacs implementation is being run on an x86_64 Linux system with Tesla S2050 GPU cards. The CUDA version is 3.1 and Gromacs is linked against OpenMM-2.0. An .mdp file is appended below. I have also tested finite values for cutoffs, but the results were worse (failures occurred more quickly). I have not been able to use the latest git version of Gromacs to test whether anything has been fixed, but will post separately to gmx-developers regarding the reasons for that soon. -Justin === md.mdp === title = Implicit solvent test ; Run parameters integrator = sd dt = 0.002 nsteps = 500 ; 1 ps (10 ns) nstcomm = 1 comm_mode = angular ; non-periodic system ; Output parameters nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 1000 ; every 2 ps nstlog = 5000 ; every 10 ps nstenergy = 1000 ; every 2 ps ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= no; starting up ; required cutoffs for implicit nstlist = 0 ns_type = grid rlist = 0 rcoulomb= 0 rvdw= 0
Re: [gmx-users] Tabulated potentials for dihedrals - regd
Dear Mark, I am very Thankful to you for your valuable suggestion. On Thu, Jun 7, 2012 at 12:04 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 7/06/2012 4:33 AM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, According to my understanding functional form of dihedral function type 9 is same as dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except the difference that function type 9 is used to handle the multiple potential functions to be applied to the single dihedreal, Is my understanding correct ?. The functional form that I am using Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 is different from the k (1 + cos(n (phi)- phi s)). I am suspecting can I use function type 9 for my function. Can you please clarify my doubt. I said last time you can use type 9. You can use high-school maths to express your equation in the form of a sum of multiple type 1, which is type 9. The additive constant only affects the total energy, which is never used for the simulation. The derivative of V is used, so the constant goes away. Mark Thank you in advance. On Mon, Jun 4, 2012 at 12:55 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). You do not need a table for this - type 9 will do the job easily, and for friendly values of phi0, there exists an equivalent form to the above that can be expressed as a Ryckaert-Belleman dihedral. See various places of manual chapters 4 and 5. I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Your table would need to be the weighted sum of the three cosines, so apparently you have not yet generated such a table. But rather than buy trouble, go and do the easier and faster solutions above :-) 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 -- 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] Warnings related to Berendsen pressure coupling and use the refcoord_scaling option
Dear Gromacs Users, I am using gromacs version 4.5.5.and running my jobs on single node with 8 cores. My system contains about 425000 atoms (protein + Lipid +SOL). I have successfully reached up to Energy minimization step.As per the suggestion by Dear Mark, I am starting my NPT equilibration with Berendsen and further with Parinello-Rahman to get the right ensemble.But when I am trying for NPT equilibration with Berendsen, getting following Warnings. WARNING 1 [file npt.mdp]: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat WARNING 2 [file npt.mdp]: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. And about 10 such LINCS warnings while running the job as shown below: Step 39, time 0.078 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.29, max 0.000473 (between atoms 890 and 891) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12050 12049 31.20.1000 0.1000 0.1000 11721 11720 46.00.1000 0.1000 0.1000 5496 5495 36.80.1000 0.1000 0.1000 With –maxwarn option I am able to run it, and output density and pressure seems perfectly alright. Based on the same I want to know:- 1. How does pressure coupling with Berendsen invalidates the true ensemble? At least for initial fixing of density and pressure? Whether to bother for above mentioned warning or ignore it? 1. Pressure coupling with absolute position restraints warning how it will lead to artifacts? How one can use refcoord_scaling option in this situation? Whether to bother for above mentioned warning or ignore it? 1. Using Berendsen with semiisotropic couple type is wrong method or no such problem? Please suggest me whether to move ahead with ignorance to the warnings or to change some parameters in mdp file? I have attached my npt.mdp file for your consideration. Thanking you In advance, Pavan Payghan npt.doc Description: MS-Word document -- 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] Warnings related to Berendsen pressure coupling and use the refcoord_scaling option
On 7/06/2012 8:33 PM, PAVAN PAYGHAN wrote: Dear Gromacs Users, I am using gromacs version 4.5.5.and running my jobs on single node with 8 cores. My system contains about 425000 atoms (protein + Lipid +SOL). I have successfully reached up to Energy minimization step.As per the suggestion by Dear Mark, I am starting my NPT equilibration with Berendsen and further with Parinello-Rahman to get the right ensemble.But when I am trying for NPT equilibration with Berendsen, getting following Warnings. WARNING 1 [file npt.mdp]: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat WARNING 2 [file npt.mdp]: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. And about 10 such LINCS warnings while running the job as shown below: Step 39, time 0.078 (ps)LINCS WARNING relative constraint deviation after LINCS: rms 0.29, max 0.000473 (between atoms 890 and 891) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12050 12049 31.20.1000 0.1000 0.1000 11721 11720 46.00.1000 0.1000 0.1000 5496 5495 36.80.1000 0.1000 0.1000 With --maxwarn option I am able to run it, and output density and pressure seems perfectly alright. Based on the same I want to know:- 1. How does pressure coupling with Berendsen invalidates the true ensemble? See manual sections for T and P coupling for introductory discussion. At least for initial fixing of density and pressure? Whether to bother for above mentioned warning or ignore it? Since you're going to do more equilibration after this, you be the judge. 2. Pressure coupling with absolute position restraints warning how it will lead to artifacts? How one can use refcoord_scaling option in this situation? See manual. Whether to bother for above mentioned warning or ignore it? Position restraints and NPT is messy. Choose your poison. 3. Using Berendsen with semiisotropic couple type is wrong method or no such problem? Please suggest me whether to move ahead with ignorance to the warnings or to change some parameters in mdp file? That's your judgement to make. How does your preparation protocol compare to the ones you have read about in the recent literature? 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] GPU crashes
On 6/7/12 3:57 AM, lloyd riggs wrote: Did you play with the time step? Just currious, but I woundered what happened with 0.0008, 0.0005, 0.0002. I found if I had a good behaving protein, as soon as I added a small (non-protein) molecule which rotated wildly while attached to the protein, it would crash unless I reduced the time step to the above when constraints were removed after EQ ... always it seemed to me it didnt like the rotation or bond angles, seeing them as a violation but acted like it was an amino acid? (the same bond type but with wider rotation as one end wasnt fixed to a chain) If your loop moves via backbone, the calculated angles, bonds or whatever might appear to the computer to be violating the parameter settings for problems, errors, etc as it cant track them fast enough over the time step. Ie atom 1-2-3 and then delta 1-2-3 with xyz parameters, but then the particular set has additional rotation, etc and may include the chain atoms which bend wildly (n-Ca-Cb-Cg maybe a dihedral) but proba! bly not this. Just a thought but probably not the right answere as well, it might be the way it is broken down (above) over GPUs, which convert everything to matricies (non-standard just for basic math operations not real matricies per say) for exicution and then some library problem which would not account for long range rapid (0.0005) movements at the chain (Ca,N,O to something else) and then tries to apply these to Cb-Cg-O-H, etc using the initial points while looking at the parameters for say a single amino acid...Maybe the constraints would cause this, which would make it a pain to EQ, but this allowed me to increase the time step, but would ruin the experiment I had worked on as I needed it unconstrained to show it didnt float away when proteins were pulled, etc...I was using a different integrator though...just normal MD. I have long wondered if constraints were properly handled by the OpenMM library. I am constraining all bonds, so in principle, dt of 0.002 should not be a problem. The note printed indicates that the constraint algorithm is changed from the one selected (LINCS) to whatever OpenMM uses (SHAKE and a few others in combination). Perhaps I can try running without constraints and a reduced dt, but I'd like to avoid it. I wish I could efficiently test to see if this behavior was GPU-specific, but unfortunately the non-GPU implementation of the implicit code can currently only be run in serial or on 2 CPU due to an existing bug. I can certainly test it, but due to the large number of atoms, it will take several days to even approach 1 ns. ANd your cutoffs for vdw, etc...Why are they 0? I dont know if this means a defautl set is then used...but if not ? Wouldnt they try integrating using both types of formula, or would it be just using coulumb or vice versa? (dont know what that would do to the code but assume it means no vdw, and all coulumb but then zeros are alwyas a problem for computers). The setup is for the all-vs-all kernels. Setting cutoffs equal to zero and using a fixed neighbor list triggers these special optimized kernels. I have also noticed that long, finite cutoffs (on the order of 4.0 nm) lead to unacceptable energy drift and structural instability in well-behaved systems (even the benchmarks). For instance, the backbone RMSD of lysozyme is twice as large in the case of a 4.0-nm cutoff relative to the all-vs-all setup, and the energy drift is quite substantial. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system
On 6/6/12 1:12 PM, Sangita Kachhap wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system (Justin A. Lemkul) 2. Segmentation fault - pdb2gmx specbond.dat (Steven Neumann) 3. energy conservation: shift vs shifted user potential (Anja Kuhnhold) 4. Cannot get correct pressure value with MTTK pressure coupling (Bao Kai) 5. Re: Cannot get correct pressure value with MTTK pressure coupling (Justin A. Lemkul) -- Message: 1 Date: Wed, 06 Jun 2012 08:56:04 -0400 From: Justin A. Lemkuljalem...@vt.edu Subject: Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system To: Discussion list for GROMACS usersgmx-users@gromacs.org Message-ID:4fcf5364@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed On 6/6/12 8:52 AM, Sangita Kachhap wrote: On 6/6/12 3:09 AM, Sangita Kachhap wrote: Hello all I have to do MD simulation of membrane protein having docked ligand in POPC lipid bilayer. I am geeting error during solvation of system: Resname of 1POPC in system_shrink1.gro converted into 1LIG I have done following: GROMACS COMMAND 1) Generate topol.top using GROMOS96 53A6 parameter set pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc at prompt select 14 2) Download: * popc128.pdb - the structure of a 128-lipid POPC bilayer * popc.itp - the moleculetype definition for POPC * lipid.itp - Berger lipid parameters from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies 3) Modify topol.top with: #include gromos53a6.ff/forcefield.itp to: #include gromos53a6_lipid.ff/forcefield.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand-full.itp ; Include POPC chain topology #include popc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp and at the end add LIG 1 in [molecules] 4) cp files aminoacids.rtp aminoacids.hdb aminoacids.c.tdb aminoacids.n.tdb aminoacids.r2b aminoacids.vsd ff_dum.itp ffnonbonded.itp ffbonded.itp forcefield.itp ions.itp spc.itp watermodels.dat from gromacs top to directory named gromos53a6_lipid.ff in working directory. Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from lipid.itp to ffnonbonded.itpffbonded.itp and create a forcefield.doc file that contains a description of the force field parameters contain GROMOS96 53A6 force field, extended to include Berger lipid parameters. Delete line ;; parameters for lipid-GROMOS interactions. and its subsequent line, change HW as H of [ nonbond_params ] 5) Generate .tpr for POPC grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1 (change OW1, HW2, HW3 to OW, HW and HW2 respectively) 6) Remove periodicity trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur compact (at command prompt select 0) 7) Oriant the protein within the same coordinate as written in end of popc128a_whole.gro editconf -f 3gd8-mod-processed.gro -o 3gd8-mod-processe_newbox.gro -c -box 6.23910 6.17970 6.91950 8) Pack lipid around protein cat 3gd8-mod-processe_newbox.gro popc128a_whole.grosystem.gro Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure and update the second line of the coordinate file (total number of atoms) accordingly. 9) Modify topol.top to add positional restrain on protein ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include DPPC chain topology #include dppc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp Genrate new positional restraint genrestr -f 3gd8-mod-processe_newbox.gro -o strong_posre.itp -fc 10 10 10 for system (protein + ligand) Add a line define = -DSTRONG_POSRES to .mdp file 10) addion POPC 128 to topol.top 11) Scale down lipid perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat 12) Solvate with water Copy vdwradii.dat from Gromacs top to working directory and change the value of C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)
Re: [gmx-users] Regarding g_sham
On 6/7/12 2:55 AM, bipin singh wrote: Hello All, I have a doubt regarding -tsham option of g_sham (single histogram analysis). While using g_sham do we need to mention the temperature at which simulation were performed or it should be the constant (298.15K) for all analysis ( no matter at what temperature simulations were performed). Well, kBT changes with temperature (obviously) so I would think it would note be useful to construct a free energy surface at 298.15 K if your simulations were done at a different temperature. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] How to set up constraint distcance pulling
Dear gmxers, I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of distance between the COMs of two molecules. However, quite strange resuluts are generated, i.e., the distance can not be fixed at the value defined by pull_init1. The pull opinions are given below. Could you please tell me how to deal with this? Thanks a lot for any reply. Chaofu Wu ;Pull opinions pull = constraint pull_geometry = distance ;pull_dim = Y Y Y pull_group0 = r1 pull_group1 = r2 pull_nstxout = 0 pull_nstfout = 5 pull_init1 = 0.80 -- Department of Chemistry and Materials Science Hunan University of Humanities, Science and Technology, Loudi 417000, the People's Republic of China (P.R. China)-- 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] How to set up constraint distcance pulling
On 6/7/12 7:38 AM, xiaowu759 wrote: Dear gmxers, I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of distance between the COMs of two molecules. However, quite strange resuluts are generated, i.e., the distance can not be fixed at the value defined by pull_init1. The pull opinions are given below. Could you please tell me how to deal with this? Thanks a lot for any reply. How far away from the target value are the results in terms of COM distance? Chaofu Wu ;Pull opinions pull = constraint pull_geometry = distance ;pull_dim = Y Y Y The comment here has no effect; pull_dim defaults to Y Y Y. pull_group0 = r1 pull_group1 = r2 pull_nstxout = 0 pull_nstfout = 5 pull_init1 = 0.80 How does this pull_init1 value compare to the COM separation in the coordinate file? If the distance is not very close, the constraint algorithm may fail. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Regarding Free Energy calculation tutorial
Dear Justin, Greetings of the day!! I am following your tutorial for the calculation of free energy change in gromacs. It says about the change in state A and state B. I have a query regarding these states. What are the 2 states A and B in the tutorial and how can I define these 2 states for my system? For example, I have a Protein-Mg-GTP complex (In initial state A, 2 specific H-bonds are absent and in the final state, these 2 H-bonds are present). So, how can I implement this for the calculation of change in free energy to my system? Thanks and Regards, Neeru Sharma CDAC, Pune, India -- 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] gmx-users Digest, Vol 98, Issue 42
Dear Mark, Thank you very much for the reply. To clarify , I have asked all the warning based questions to get acknowledged with your expert opinion, apart from the manual based view. According to your suggestion NPT with Position restraints is messy,but still I have seen lots of manual/tutorial (including Bevans Lab ) suggesting the position restraining of protein during NVT as well as NPT. That is the reason I have followed the same. Please clarify your view on this matter. Thak you very much in advance. Pavan Payghan On Thu, Jun 7, 2012 at 4:58 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Warnings related to Berendsen pressure coupling and use the refcoord_scaling option (Mark Abraham) 2. Re: GPU crashes (Justin A. Lemkul) 3. Re: Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system (Justin A. Lemkul) -- Message: 1 Date: Thu, 07 Jun 2012 20:42:47 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Warnings related to Berendsen pressure coupling anduse the refcoord_scaling option To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fd085a7.5000...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 7/06/2012 8:33 PM, PAVAN PAYGHAN wrote: Dear Gromacs Users, I am using gromacs version 4.5.5.and running my jobs on single node with 8 cores. My system contains about 425000 atoms (protein + Lipid +SOL). I have successfully reached up to Energy minimization step.As per the suggestion by Dear Mark, I am starting my NPT equilibration with Berendsen and further with Parinello-Rahman to get the right ensemble.But when I am trying for NPT equilibration with Berendsen, getting following Warnings. WARNING 1 [file npt.mdp]: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat WARNING 2 [file npt.mdp]: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. And about 10 such LINCS warnings while running the job as shown below: Step 39, time 0.078 (ps)LINCS WARNING relative constraint deviation after LINCS: rms 0.29, max 0.000473 (between atoms 890 and 891) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12050 12049 31.20.1000 0.1000 0.1000 11721 11720 46.00.1000 0.1000 0.1000 5496 5495 36.80.1000 0.1000 0.1000 With --maxwarn option I am able to run it, and output density and pressure seems perfectly alright. Based on the same I want to know:- 1. How does pressure coupling with Berendsen invalidates the true ensemble? See manual sections for T and P coupling for introductory discussion. At least for initial fixing of density and pressure? Whether to bother for above mentioned warning or ignore it? Since you're going to do more equilibration after this, you be the judge. 2. Pressure coupling with absolute position restraints warning how it will lead to artifacts? How one can use refcoord_scaling option in this situation? See manual. Whether to bother for above mentioned warning or ignore it? Position restraints and NPT is messy. Choose your poison. 3. Using Berendsen with semiisotropic couple type is wrong method or no such problem? Please suggest me whether to move ahead with ignorance to the warnings or to change some parameters in mdp file? That's your judgement to make. How does your preparation protocol compare to the ones you have read about in the recent literature? Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120607/bb5024ac/attachment-0001.html -- Message: 2 Date: Thu, 07 Jun 2012 07:25:31 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] GPU crashes To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fd08fab.5000...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed On 6/7/12 3:57 AM, lloyd riggs wrote: Did you play with the time step? Just currious, but I woundered what happened with 0.0008, 0.0005, 0.0002. I found
Re: [gmx-users] Regarding Free Energy calculation tutorial
On 6/7/12 8:26 AM, neeru sharma wrote: Dear Justin, Greetings of the day!! I am following your tutorial for the calculation of free energy change in gromacs. It says about the change in state A and state B. I have a query regarding these states. What are the 2 states A and B in the tutorial and how can I define these 2 states for my system? The changes applied between state A and B are defined in the .mdp file based on the couple-lambda0 and couple-lambda1 settings. These are used to transform either vdW or Coulombic interactions. If you need to make some other type of change (i.e. a mutation), then you would do so in the topology, setting B-state parameters explicitly. For example, I have a Protein-Mg-GTP complex (In initial state A, 2 specific H-bonds are absent and in the final state, these 2 H-bonds are present). So, how can I implement this for the calculation of change in free energy to my system? This doesn't sound like something that can be done with the decoupling technique; it sounds to me more like a structural change. Perhaps you can do some careful calculations using the pull code, but it is not clear to me what you are trying to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] How to set up constraint distcance pulling
Date: Thu, 07 Jun 2012 07:59:27 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] How to set up constraint distcance pulling To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fd0979f.4020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Thank you very much! On 6/7/12 7:38 AM, xiaowu759 wrote: Dear gmxers, I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of distance between the COMs of two molecules. However, quite strange resuluts are generated, i.e., the distance can not be fixed at the value defined by pull_init1. The pull opinions are given below. Could you please tell me how to deal with this? Thanks a lot for any reply. How far away from the target value are the results in terms of COM distance? A: very far, several hundreds vs. 0.8 nm Chaofu Wu ;Pull opinions pull = constraint pull_geometry = distance ;pull_dim = Y Y Y The comment here has no effect; pull_dim defaults to Y Y Y. A: Yes pull_group0 = r1 pull_group1 = r2 pull_nstxout = 0 pull_nstfout = 5 pull_init1 = 0.80 How does this pull_init1 value compare to the COM separation in the coordinate file? If the distance is not very close, the constraint algorithm may fail. A: The COM separation in the coordinate file is 0.567 nm, which should be not too larger than 0.80 defined by pull_init1. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Department of Chemistry and Materials Science Hunan University of Humanities, Science and Technology, Loudi 417000, the People's Republic of China (P.R. China)-- 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] How to set up constraint distcance pulling
On 6/7/12 9:14 AM, xiaowu759 wrote: Date: Thu, 07 Jun 2012 07:59:27 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] How to set up constraint distcance pulling To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4fd0979f.4020...@vt.edu mailto:4fd0979f.4020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Thank you very much! On 6/7/12 7:38 AM, xiaowu759 wrote: Dear gmxers, I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of distance between the COMs of two molecules. However, quite strange resuluts are generated, i.e., the distance can not be fixed at the value defined by pull_init1. The pull opinions are given below. Could you please tell me how to deal with this? Thanks a lot for any reply. How far away from the target value are the results in terms of COM distance? A: very far, several hundreds vs. 0.8 nm A distance of several hundred nm would indicate to me that the system blew up. Chaofu Wu ;Pull opinions pull = constraint pull_geometry = distance ;pull_dim = Y Y Y The comment here has no effect; pull_dim defaults to Y Y Y. A: Yes pull_group0 = r1 pull_group1 = r2 pull_nstxout = 0 pull_nstfout = 5 pull_init1 = 0.80 How does this pull_init1 value compare to the COM separation in the coordinate file? If the distance is not very close, the constraint algorithm may fail. A: The COM separation in the coordinate file is 0.567 nm, which should be not too larger than 0.80 defined by pull_init1. That's a 29% difference, which is quite large. If constraints are not easily satisfied, the simulation can blow up. Your statement above makes that seem very likely. Your restraint distance should match the actual coordinates very closely, otherwise you will likely need to equilibrate better under e.g. an umbrella potential and relatively weak force constant to obtain better starting structures if you're intent on using a rigid constraint for the PMF calculation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] dssp doubt
Hi all, I downloaded the original form of DSSP which is recently called DSSPold. Whenever I use the following: *do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm * It selects Protein by it-self without any control from me. I want to choose from the list, for example not protein but C-alpha. To solve this probIem, I prepared the index file which includes only C-alphas of my system. Then, I use the following: *do_dssp -s topol.tpr -f traj.xtc -n C_alpha.ndx* I get the below fatal error: Program do_dssp, VERSION 4.5.4 Source code file: do_dssp.c, line: 566 Fatal error: Failed to execute command: /home_palamut2/mguler/dssp/dsspcmbi -na ddcblxTU ddq8aNVV /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Are there any suggestions or corrections? Thanks in advance.. Turgay -- 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] dssp doubt
On 6/7/12 10:07 AM, Turgay Cakmak wrote: Hi all, I downloaded the original form of DSSP which is recently called DSSPold. Whenever I use the following: *do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm * It selects Protein by it-self without any control from me. I want to choose from the list, for example not protein but C-alpha. That shouldn't happen. You should be prompted for a selection. Note that selecting only C-alpha atoms will not work. DSSP requires all MainChain atoms to be considered, since the secondary structure criteria are based on hydrogen bonding distances. An incorrect selection could explain the error you get below. -Justin To solve this probIem, I prepared the index file which includes only C-alphas of my system. Then, I use the following: *do_dssp -s topol.tpr -f traj.xtc -n C_alpha.ndx* I get the below fatal error: Program do_dssp, VERSION 4.5.4 Source code file: do_dssp.c, line: 566 Fatal error: Failed to execute command: /home_palamut2/mguler/dssp/dsspcmbi -na ddcblxTU ddq8aNVV /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Are there any suggestions or corrections? Thanks in advance.. Turgay -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: gmx-users Digest, Vol 98, Issue 44
Message: 1 Date: Thu, 07 Jun 2012 08:53:22 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Regarding Free Energy calculation tutorial To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fd0a442.6000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 6/7/12 8:26 AM, neeru sharma wrote: Dear Justin, Greetings of the day!! I am following your tutorial for the calculation of free energy change in gromacs. It says about the change in state A and state B. I have a query regarding these states. What are the 2 states A and B in the tutorial and how can I define these 2 states for my system? The changes applied between state A and B are defined in the .mdp file based on the couple-lambda0 and couple-lambda1 settings. These are used to transform either vdW or Coulombic interactions. If you need to make some other type of change (i.e. a mutation), then you would do so in the topology, setting B-state parameters explicitly. For example, I have a Protein-Mg-GTP complex (In initial state A, 2 specific H-bonds are absent and in the final state, these 2 H-bonds are present). So, how can I implement this for the calculation of change in free energy to my system? This doesn't sound like something that can be done with the decoupling technique; it sounds to me more like a structural change. Perhaps you can do some careful calculations using the pull code, but it is not clear to me what you are trying to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Thanks for the reply. Well,yes it is more of the strutural change in case of my case which can also be quantified in terms of presence and absence of these 2 H-bonds. And as the two structures are distinct from each other too, there has to be some energy change which I want to calculate too. Moreover, this structure change and the appearance of these H-bonds take long time and cross a energetic barrier too, I am trying to calculate this energy barrier too. Regarding the pull code, I will also try it for my system --- Neeru -- 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] dssp doubt
Hi Justin, Thank you for your descriptive reply. I prepared new index.file which includes mainchain, and when I used the do_dssp with -n index.ndx, it worked. But, if I doesn't use the index file, again, the Protein is selected by the system. It is weird.. Best regards, Deniz On Thu, Jun 7, 2012 at 5:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/7/12 10:07 AM, Turgay Cakmak wrote: Hi all, I downloaded the original form of DSSP which is recently called DSSPold. Whenever I use the following: *do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm * It selects Protein by it-self without any control from me. I want to choose from the list, for example not protein but C-alpha. That shouldn't happen. You should be prompted for a selection. Note that selecting only C-alpha atoms will not work. DSSP requires all MainChain atoms to be considered, since the secondary structure criteria are based on hydrogen bonding distances. An incorrect selection could explain the error you get below. -Justin To solve this probIem, I prepared the index file which includes only C-alphas of my system. Then, I use the following: *do_dssp -s topol.tpr -f traj.xtc -n C_alpha.ndx* I get the below fatal error: Program do_dssp, VERSION 4.5.4 Source code file: do_dssp.c, line: 566 Fatal error: Failed to execute command: /home_palamut2/mguler/dssp/**dsspcmbi -na ddcblxTU ddq8aNVV /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors Are there any suggestions or corrections? Thanks in advance.. Turgay -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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
[gmx-users] About Umbrella sampling
Dear justin Thank you for your previous Valuable reply. To do umbrella sampling should i run more number of steps than i run in Umbrella pulling ? otherwise if i use lesser number of steps in Umbrella sampling than pulling will it affect result Is there is any rule between number of steps and dt in umbrella pulling and umbrella sampling? Thanks in Advance -- 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] About Umbrella sampling
On 6/7/12 12:26 PM, vidhya sankar wrote: Dear justin Thank you for your previous Valuable reply. To do umbrella sampling should i run more number of steps than i run in Umbrella pulling ? That depends on how many steps were used for the pulling. Also note that the pulling step represents just one possible way to generate initial configurations and is not necessarily even required, so you shouldn't necessarily base a whole lot on this process. otherwise if i use lesser number of steps in Umbrella sampling than pulling will it affect result You shouldn't try to connect the two. Is there is any rule between number of steps and dt in umbrella pulling and umbrella sampling? The same rules as any simulation apply. Parameters like dt are chosen based on what gives a stable result. The length of the simulation depends on your convergence criteria. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: Thermodynamic Integration Glu - Ala Mutation
Any suggestions on this topic? Thanks again for your time. Dear Gromacs Users, I am trying to find out the relative free energy difference of binding of a ligand with wild type protein (Glutamate residue) and mutant protein (Alanine residue). For charge part of the mutation, this is what I'm planning to do: ; residue 40 GLU rtp GLU q -1.0 552 opls_238 40GLU N 191 -0.514.0067 opls_238-0.5 14.0067 ; qtot 0.5 553 opls_241 40GLU H 1910.3 1.008 opls_241 0.3 1.008 ; qtot 0.8 554 opls_224B 40GLU CA191 0.14 12.011 opls_224B0.14 12.011 ; qtot 0.94 555 opls_140 40GLU HA191 0.06 1.008 opls_140 0.061.008 ; qtot 1 556 opls_136 40GLU CB192 -0.12 12.011 opls_135 -0.18 12.011 ; qtot 0.88 557 opls_140 40GLUHB1192 0.06 1.008 opls_140 0.061.008 ; qtot 0.94 558 opls_140 40GLUHB2192 0.06 1.008 opls_140 0.061.008 ; qtot 1 559 opls_274 40GLU CG193 -0.22 12.011 opls_140 0.061.008 ; qtot 0.78 560 opls_140 40GLUHG1193 0.06 1.008 DUM_1400.0 1.008 ; qtot 0.84 561 opls_140 40GLUHG2193 0.06 1.008 DUM_1400.0 1.008 ; qtot 0.9 562 opls_271 40GLU CD 1940.7 12.011 DUM_2710.0 12.011 ; qtot 1.6 563 opls_272 40GLUOE1194 -0.815.9994 DUM_272 0.0 15.9994 ; qtot 0.8 564 opls_272 40GLUOE2194 -0.815.9994 DUM_2720.0 15.9994 ; qtot 0 565 opls_235 40GLU C 1950.5 12.011 opls_235 0.5 12.011 ; qtot 0.5 566 opls_236 40GLU O 195 -0.515.9994 opls_236-0.515.9994 ; qtot 0 I added the DUM_140, DUM_271,DUM_272 atomtypes in ffnonbonded.itp. Further I added the bondtypes, angletypes and dihedraltypes in ffbonded.itp for state B. In order to maintain the electroneutrality, I am mutating a K+ ion to dummy as well. For the K+ going to dummy, I added a DUM_408 atomtype as well. *The questions I have are as follows:* *During the charge mutation will my dummy atoms have sigma and epsilon as 0.0? Since Ala residue does not have Cgamma, Cdelta and the oxygen as well as the Hgamma, all the dummy atoms should have sigma and epsilon as zero. Am I correct for this assumption?* *Further as I am mutating one ion, I dont want the mutating ion to come close to other ions (I have three K+ ions as my protein has -3 charge) as well as the protein atoms. Hence I'm having position restraints on the three ions. * *For the ion that is mutating to dummy, should I have have position restraints on dummy atom as well for the B state topology?* The section of topology for the K+ going to dummy is as follows: [ moleculetype ] ; Namenrexcl KM 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls-408 1 KMKM1 139.0983 DUM_408 0.0 39.0983 #ifdef POSRES_ION ; Position restraint for each Potassium ion [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 0 0 0 #endif Here I defined the KM as K+ that will go to dummy and other two K+ ions are represented as regular K+ ions. I'm pasting the regular K+ ion part of the topology below. [ moleculetype ] ; Namenrexcl K 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_408 1 K K1 139.0983 #ifdef POSRES_ION ; Position restraint for each Potassium ion [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif Let me know if you need more information. Thanks for your time, Regards Sai -- 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] Atomtype OW_tip4p not found
From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, June 6, 2012 4:08 PM Subject: Re: [gmx-users] Atomtype OW_tip4p not found On 6/6/12 7:36 AM, Amir Abbasi wrote: *From:* Justin A. Lemkul jalem...@vt.edu *To:* Amir Abbasi amir.abbas...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, June 6, 2012 3:58 PM *Subject:* Re: [gmx-users] Atomtype OW_tip4p not found On 6/6/12 7:19 AM, Amir Abbasi wrote: Hi! I use tleap to generate topology file of a RNA molecule with parmbsc0 ff. Then I generate .gro and .top files of that with amb2gmx.pl http://amb2gmx.pl. I'm manually add this lines to .top file ; Include water topology #include amber99sb.ff/tip4p.itp ; Include topology for ions #include amber99sb.ff/ions.itp but after running this code: grompp -f ions.mdp -c ribozyme_solv.gro -p ribozyme.top -o ions.tpr I've got this error message: Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1166 Fatal error: Atomtype OW_tip4p not found what should I do? If I recall my Amber evolution correctly, parmbsc0 and Amber99SB are different entities, so you may have some inconsistencies in your force field calls. Which of the Amber force fields in Gromacs have you called (earlier in the topology)? The OW_tip4p atom type exists in Amber99SB, so I don't know the origin of the error. -Justin I've Removed these lines from .top file ; Include water topology #include amber99sb.ff/tip4p.itp ; Include topology for ions #include amber99sb.ff/ions.itp But this error occured: Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1987 Fatal error: No such moleculetype SOL what's the true way to add solvent molecules to my system? I want to use parmbsc0 ff that's not included in gromacs and I use it with amb2gmx Please answer the question posted above by posting a relevant topology snippet. It's hard (impossible) to help you while working in the dark. Presumably you have some force field you are calling - what is it? Removal of these lines will not solve the problem, as you can see. You need to #include a water model of some sort to define what parameters water will have, but it needs to be consistent with whatever force field you are using or have otherwise constructed. -Justin this is my topology file (generated by amb2gmx_dihed_old.pl): ; rna.top created by rdparm2gmx.pl Thu May 24 19:07:56 IRDT 2012 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon HO HO 0. 0. A 0.0e+00 0.0e+00 NC NC 0. 0. A 3.25000e-01 7.11280e-01 H5 H5 0. 0. A 2.42146e-01 6.27600e-02 N2 N2 0. 0. A 3.25000e-01 7.11280e-01 CB CB 0. 0. A 3.39967e-01 3.59824e-01 CK CK 0. 0. A 3.39967e-01 3.59824e-01 N* N* 0. 0. A 3.25000e-01 7.11280e-01 OS OS 0. 0. A 3.1e-01 7.11280e-01 CT CT 0. 0. A 3.39967e-01 4.57730e-01 C C 0. 0. A 3.39967e-01 3.59824e-01 NB NB 0. 0. A 3.25000e-01 7.11280e-01 CA CA 0. 0. A 3.39967e-01 3.59824e-01 OH OH 0. 0. A 3.06647e-01 8.80314e-01 NA NA 0. 0. A 3.25000e-01 7.11280e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 CM CM 0. 0. A 3.39967e-01 3.59824e-01 H1 H1 0. 0. A 2.47135e-01 6.56888e-02 O2 O2 0. 0. A 2.95992e-01 8.78640e-01 P P 0. 0. A 3.74177e-01 8.36800e-01 H2 H2 0. 0. A 2.29317e-01 6.56888e-02 HA HA 0. 0. A 2.59964e-01 6.27600e-02 H4 H4 0. 0. A 2.51055e-01 6.27600e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 [ moleculetype ] ; Name nrexcl solute 3 there is not any force field included. I want to use parmbsc0 ff thats not included in gromacs. I build topology file in tleap (part of ambertools) then convert it to gromacs topology file.-- 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
Re: [gmx-users] Atomtype OW_tip4p not found
On 6/7/12 6:18 PM, Amir Abbasi wrote: *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, June 6, 2012 4:08 PM *Subject:* Re: [gmx-users] Atomtype OW_tip4p not found On 6/6/12 7:36 AM, Amir Abbasi wrote: *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Amir Abbasi amir.abbas...@yahoo.com mailto:amir.abbas...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Wednesday, June 6, 2012 3:58 PM *Subject:* Re: [gmx-users] Atomtype OW_tip4p not found On 6/6/12 7:19 AM, Amir Abbasi wrote: Hi! I use tleap to generate topology file of a RNA molecule with parmbsc0 ff. Then I generate .gro and .top files of that with amb2gmx.pl http://amb2gmx.pl http://amb2gmx.pl. I'm manually add this lines to .top file ; Include water topology #include amber99sb.ff/tip4p.itp ; Include topology for ions #include amber99sb.ff/ions.itp but after running this code: grompp -f ions.mdp -c ribozyme_solv.gro -p ribozyme.top -o ions.tpr I've got this error message: Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1166 Fatal error: Atomtype OW_tip4p not found what should I do? If I recall my Amber evolution correctly, parmbsc0 and Amber99SB are different entities, so you may have some inconsistencies in your force field calls. Which of the Amber force fields in Gromacs have you called (earlier in the topology)? The OW_tip4p atom type exists in Amber99SB, so I don't know the origin of the error. -Justin I've Removed these lines from .top file ; Include water topology #include amber99sb.ff/tip4p.itp ; Include topology for ions #include amber99sb.ff/ions.itp But this error occured: Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1987 Fatal error: No such moleculetype SOL what's the true way to add solvent molecules to my system? I want to use parmbsc0 ff that's not included in gromacs and I use it with amb2gmx Please answer the question posted above by posting a relevant topology snippet. It's hard (impossible) to help you while working in the dark. Presumably you have some force field you are calling - what is it? Removal of these lines will not solve the problem, as you can see. You need to #include a water model of some sort to define what parameters water will have, but it needs to be consistent with whatever force field you are using or have otherwise constructed. -Justin this is my topology file (generated by amb2gmx_dihed_old.pl): ; rna.top created by rdparm2gmx.pl Thu May 24 19:07:56 IRDT 2012 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon HO HO 0. 0. A 0.0e+00 0.0e+00 NC NC 0. 0. A 3.25000e-01 7.11280e-01 H5 H5 0. 0. A 2.42146e-01 6.27600e-02 N2 N2 0. 0. A 3.25000e-01 7.11280e-01 CB CB 0. 0. A 3.39967e-01 3.59824e-01 CK CK 0. 0. A 3.39967e-01 3.59824e-01 N* N* 0. 0. A 3.25000e-01 7.11280e-01 OS OS 0. 0. A 3.1e-01 7.11280e-01 CT CT 0. 0. A 3.39967e-01 4.57730e-01 C C 0. 0. A 3.39967e-01 3.59824e-01 NB NB 0. 0. A 3.25000e-01 7.11280e-01 CA CA 0. 0. A 3.39967e-01 3.59824e-01 OH OH 0. 0. A 3.06647e-01 8.80314e-01 NA NA 0. 0. A 3.25000e-01 7.11280e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 CM CM 0. 0. A 3.39967e-01 3.59824e-01 H1 H1 0. 0. A 2.47135e-01 6.56888e-02 O2 O2 0. 0. A 2.95992e-01 8.78640e-01 P P 0. 0. A 3.74177e-01 8.36800e-01 H2 H2 0. 0. A 2.29317e-01 6.56888e-02 HA HA 0. 0. A 2.59964e-01 6.27600e-02 H4 H4 0. 0. A 2.51055e-01 6.27600e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 [ moleculetype ] ; Name nrexcl solute 3 there is not any force field included. I want to use parmbsc0 ff thats not included in gromacs. I build topology file in tleap (part of ambertools) then convert it to gromacs topology file. Then you need to add all appropriate parameters for the missing atom types. As you can see from the [atomtypes] directive above, you have not declared OW_tip4p. Anything that you need to use later on must be declared at the beginning of the topology. See Chapter 5 of the manual for the required format and sequence of directives. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] qmmm and real-life meaning of null lennard-jones parameters
On 6/7/12 7:28 PM, Edward Deira wrote: Dear all, I'm currently starting to dwell deeper in MD, and I'm taking some time to understand what's going on inside the gromacs black-box. In one of those dwellings, I came across an older post [http://www.mail-archive.com/gmx-users@gromacs.org/msg42568.html] which reads: Question: 4. In ffnonbonded.itp, why are both sigma and epsilon set to zero for HW (opls_117)? This seems to imply that, as far as Lennard-Jones interactions are concerned, the hydrogens on the waters don't exist. Or, in other words, in the absence of charges, the hydrogens don't feel the hydrogens, the hydrogens don't feel the oxygens, and the oxygens don't feel the hydrogens. In other words, the hydrogens interact with the world only via electrostatic (Coulombic) interactions. Is this a correct interpretation?Correct. Many force fields do this. Answer: So, my question, if a question at all: Suppose I have a regular protein and put inside some metal atom that will coordinate with some O and N atoms from the side chains. If the sigma and epsilon for that metal are null, than the metal - sidechains interactions are exclusively electrostatic. Does this make sense ? What are the implications of this for the coordination chemistry of that metal - sidechain complex ? On the side: suppose I want some non parameterized metal atom, say W, for which I will compute all the other parameters in the same/similar way described in the force field papers, but for which no experimental data are available for me to compare computable meaningful sigma and epsilon values. Can I just sigma and epsilon to zero ? Or should I do qmmm to have W in the qm part ? The fact that the LJ parameters for H are zero derives from its size. The environment is more strongly influenced by the heavy atom to which H is bonded. In the case of a larger metal ion, I would seriously doubt that setting LJ parameters to zero is valid. It's quite convenient, but in most force fields, all metal ions have some LJ parameters. Perhaps investigating how those parameters were derived would be useful. For what it's worth, I believe the origin of the zero-LJ H parameters comes from this work: http://pubs.acs.org/doi/abs/10.1021/ja00824a004 Also, from the few tutorials and from the manual, I have the impression that even for qmmm with gromacs and mopac i still need force field parameters for the qm part, is this true ? Or i just need to include a qmmm section in all mdp files, including the first ion adding and energy minimization steps ? Sorry for the naivety in this, but i've only made regular protein MD so far. I've never done any QM/MM, but my assumption would be that you have to have some valid topology to start with. Perhaps someone else can comment on this methodological issue. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Trouble with packing lipids around a protein using InflateGRO
Hi, I am working through the KALP-15 in DPPC tutorial (only using a different protein) and having difficulties in packing the lipids around the protein. After I scaled the lipid positions by a factor of 4 (perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) and ran energy minimizations (mdrun -v -deffnm em) I tried to scale down the lipids by a factor 0.95. However, I did not get the result of the minimization (confout.gro). I then received this error: Ek! No confout.gro at all! Died at inflategro.pl line 81. When researching this, I found this comment about the same issue I am having troubles with, that could not have been the command you entered, because inflategro.pl is looking for confout.gro, which you have not specified in the command. Any suggestions? Thanks! -- View this message in context: http://gromacs.5086.n6.nabble.com/Trouble-with-packing-lipids-around-a-protein-using-InflateGRO-tp4998194.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Trouble with packing lipids around a protein using InflateGRO
On 6/7/12 7:48 PM, Erica Hicks wrote: Hi, I am working through the KALP-15 in DPPC tutorial (only using a different protein) and having difficulties in packing the lipids around the protein. After I scaled the lipid positions by a factor of 4 (perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) and ran energy minimizations (mdrun -v -deffnm em) I tried to scale down the lipids by a factor 0.95. However, I did not get the result of the minimization (confout.gro). I then received this error: Ek! No confout.gro at all! Died at inflategro.pl line 81. When researching this, I found this comment about the same issue I am having troubles with, that could not have been the command you entered, because inflategro.pl is looking for confout.gro, which you have not specified in the command. Any suggestions? If you ran mdrun -v -deffnm em then your coordinate file is not named confout.gro, it is name em.gro. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Error in grompp steps of position restrained
Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Error message: --- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group CA not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- 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] Error in grompp steps of position restrained
On 8/06/2012 12:23 PM, Malai wrote: Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Error message: --- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group CA not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your .mdp file referred to a group for which grompp could find no definition. Choose a better group or make a definition. 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] Error in grompp steps of position restrained
Dear Mark, Thanks for mail. you mean I need to define in mdp file?. Can you please guide me how to do that. Thanks. On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/06/2012 12:23 PM, Malai wrote: Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Error message: --**- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group CA not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- Your .mdp file referred to a group for which grompp could find no definition. Choose a better group or make a definition. Mark -- 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
[gmx-users] Re: gmx-users Digest, Vol 98, Issue 42
On 7/06/2012 10:51 PM, PAVAN PAYGHAN wrote: Dear Mark, Thank you very much for the reply. To clarify , I have asked all the warning based questions to get acknowledged with your expert opinion, apart from the manual based view. According to your suggestion NPT with Position restraints is messy,but still I have seen lots of manual/tutorial (including Bevans Lab ) suggesting the position restraining of protein during NVT as well as NPT. That is the reason I have followed the same. Please clarify your view on this matter. It depends. If you need to fix your volume significantly, then trying to do so while using position restraints is somewhat asking for trouble and you should either give up position restraints or start again and get the volume closer to correct in the first place. (Those tutorials have likely managed this issue for you in the background.) Otherwise, use a different type of refcoord_scaling like the warning said. The existence of this mailing list is no substitute for doing basic background reading in (at least) the manual :-) 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] Error in grompp steps of position restrained
On 8/06/2012 12:34 PM, Malai wrote: Dear Mark, Thanks for mail. you mean I need to define in mdp file?. No. Using one of the two ways I suggested earlier depend what you're actually trying to do, but since your intention in using the CA group is unknown to us, you're preventing yourself getting specific help. Can you please guide me how to do that. Thanks. http://www.gromacs.org/Documentation/File_Formats/Index_File Mark On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 8/06/2012 12:23 PM, Malai wrote: Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Error message: --- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group CA not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your .mdp file referred to a group for which grompp could find no definition. Choose a better group or make a definition. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- 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] Error in grompp steps of position restrained
Dear MARK, Dear Mark, Thanks for mail. you mean I need to define in mdp file?. No. Using one of the two ways I suggested earlier depend what you're actually trying to do, but since your intention in using the CA group is unknown to us, you're preventing yourself getting specific help. The error is CA index file. So my intention is to use CA group and avoid the error. please suggest me how to use grompp or make CA index file for grompp in position restrained step. Can you please guide me how to do that. Thanks. http://www.gromacs.org/Documentation/File_Formats/Index_File so i need to make index files for CA atoms of protein using make_ndx for CA. can you please explain how to make index file for CA using make_ndx. Thanks for help. Mark On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/06/2012 12:23 PM, Malai wrote: Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Error message: --- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group CA not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your .mdp file referred to a group for which grompp could find no definition. Choose a better group or make a definition. 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 -- 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] query on table potential
Hi, I am trying to use a table potential implementing Weeks-Chandler-Anderson (WCA) interaction between a solute and all atoms of a solvent like TIP3P water ( with nonzero interaction in the Hydrogen atoms) . But, I am having a trouble in specifying energy groups required for table potential. Here is the problem: I have two atom types in water : OW and HW. and one atom type in solute : POL Now, I want to use two Table potentials with WCA interactions between a) POL HW and b) POL OW So, I created two table potential files: table_POL_HW.xvg and table_POL_OW.xvg and then in the .mdp file, I specified energygrps = POL OW HW energygrps_table = POL OW POL HW But, compiling the .mdp file using grompp ( version 4.5.4) gives me following error Fatal error: atoms 33 and 34 in charge group 1 of molecule type 'SOL' are in different energy groups Clearly, using OW and HW as separate energy groups is causing the problem. So, I am looking for an option on how I can use the table potential between solute and each atoms of solvent. Any help will be appreciated. Sanku-- 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] query on table potential
On 8/06/2012 1:09 PM, Sanku M wrote: Hi, I am trying to use a table potential implementing Weeks-Chandler-Anderson (WCA) interaction between a solute and all atoms of a solvent like TIP3P water ( with nonzero interaction in the Hydrogen atoms) . But, I am having a trouble in specifying energy groups required for table potential. Here is the problem: I have two atom types in water : OW and HW. and one atom type in solute : POL Now, I want to use two Table potentials with WCA interactions between a) POL HW and b) POL OW So, I created two table potential files: table_POL_HW.xvg and table_POL_OW.xvg and then in the .mdp file, I specified energygrps = POL OW HW energygrps_table = POL OW POL HW But, compiling the .mdp file using grompp ( version 4.5.4) gives me following error Fatal error: atoms 33 and 34 in charge group 1 of molecule type 'SOL' are in different energy groups Clearly, using OW and HW as separate energy groups is causing the problem. So, I am looking for an option on how I can use the table potential between solute and each atoms of solvent. Energy groups can only be unions of complete charge groups. So your energy groups require that you split the solvent charge group. The solvent charge groups are defined in its [moleculetype]. Splitting will mean that you will get integration artefacts at the cut-off unless you use a proper long-ranged electrostatic method (i.e. an Ewald family method). 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
[gmx-users] Regarding error
Dear all gromacs users, While running the grompp commond after addition of counter ions i am getting the following error. Fatal error: number of coordinates in coordinate file (3ASW_ion.gro, 178301) does not match topology (3ASW.top, 178293) Here i am sending my .top file,kindly tell me how to overcome this error. ; ; File '3ASW.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Sat Jun 9 10:36:25 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f 3ASW.pdb -o 3ASW.gro -p 3ASW.top -missing ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp ; Include chain topologies #include 3ASW_Protein_chain_A.itp #include 3ASW_Protein_chain_B.itp ; Include water topology #include gromos43a1.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp ;#include ions.itp [ system ] ; Name CLUMPING FACTOR B; TAIL REGION DERIVED PEPTIDE in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 129 SOL 5 SOL 58209 NA ions 8 /Add NA ions Suryanarayana Seera, JRF, India. -- 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] Regarding error
Have you incorrectly changed the numbers in the topology, the difference in the number is 8, so it appears your coordinate file contains 8 more atoms than the topology. You will have to work out how that is. Catch ya, Dr. Dallas Warren Drug Discovery Biology 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 Seera Suryanarayana Sent: Friday, 8 June 2012 3:32 PM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding error Dear all gromacs users, While running the grompp commond after addition of counter ions i am getting the following error. Fatal error: number of coordinates in coordinate file (3ASW_ion.gro, 178301) does not match topology (3ASW.top, 178293) Here i am sending my .top file,kindly tell me how to overcome this error. ; ; File '3ASW.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Sat Jun 9 10:36:25 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f 3ASW.pdb -o 3ASW.gro -p 3ASW.top -missing ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp ; Include chain topologies #include 3ASW_Protein_chain_A.itp #include 3ASW_Protein_chain_B.itp ; Include water topology #include gromos43a1.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp ;#include ions.itp [ system ] ; Name CLUMPING FACTOR B; TAIL REGION DERIVED PEPTIDE in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 129 SOL 5 SOL 58209 NA ions 8 /Add NA ions Suryanarayana Seera, JRF, India. -- 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
