[gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints
Hi, I minimised a heterogenous lipid system of 1464 DOPC and DOPG and applied position restraints as well as had vdwradii.dat file for genbox step. Yet after minimisation, there are gaps between the lipid molecules. Pls suggest a remedy. -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS
eRROR OBTAINED DURING NVT: Water molecule starting at atom 673675 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. NVT CONDITIONS WERE : n for B2AR-POPC system define = -DPOSRES ; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator = md; Algorithm ("md" = molecular dynamics [leap-frog integrator]; "md-vv" = md using velocity verlet; sd = stochastic dynamics) dt = 0.002 ; Time-step (ps) nsteps = 25; Number of steps to run (0.002 * 25 = 500 ps) ; Parameters controlling output writing nstxout = 1000 ; Write coordinates to output .trr file every 2 ps nstvout = 1000 ; Write velocities to output .trr file every 2 ps nstenergy = 1000 ; Write energies to output .edr file every 2 ps nstlog = 1000 ; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid ; Neighbor list search method (simple, grid) nstlist = 5 ; Neighbor list update frequency (after every given number of steps) rlist = 1.2 ; Neighbor list search cut-off distance (nm) rcoulomb= 1.2 ; Short-range Coulombic interactions cut-off distance (nm) rvdw= 1.2 ; Short-range van der Waals cutoff distance (nm) pbc = xyz ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) ; Parameters for treating bonded interactions continuation= no; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 2 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 8 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = V-rescale ; Modified Berendsen thermostat using velocity rescaling tc-grps = Protein DOPC SOL_NA ; Define groups to be coupled separately to temperature bath tau_t = 0.1 0.1 0.1 ; Group-wise coupling time constant (ps) ref_t = 300 300 300 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = no; Under NVT conditions pressure coupling is not done -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg
i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force = 7.8095098e+00 Should i go ahead with NVT and NPT? -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Need of mdp files
Hi, I am trying to simulate a peripheral membrane protein in a heterogenous lipid bilayer of DOPC and DOPG using charmm 36 force field in GROMACS. i need mdp files for NPT, NVT, steep and MD to check whether the conditions i am using to simulate my system are appropriate or not. -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein
Dear gromacs users, I am trying to run a coarse grained simulation of a membrane protein in a mixed lipid billayer using martini model. I have already performed all the equilibration steps successfully on my desktop. However, when i try to execute its production run in parallel it complains of LINCS warning and terminates at step 0. But on the contrary, it runs on the desktop successfully. Kindly suggest something and please let me know if any more information is required from my side. Thanks!! Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein
Dear users, I am trying to run a coarse grained simulation of a membrane protein in a mixed lipid billayer using martini model 2.2. I have already performed all the equilibration steps successfully on my desktop with GROMACS 5.1.0. However, when i try to execute its production run in parallel(having gromacs 5.1 version installed) it complains of LINCS warning and terminates at step 0. But on the contrary, it runs on the desktop successfully. Kindly suggest something and please let me know if any more information is required from my side. Thanks!! Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar wrote: > Dear gromacs users, > > I am trying to run a coarse grained simulation of a membrane protein in a > mixed lipid billayer using martini model. I have already performed all the > equilibration steps successfully on my desktop. However, when i try to > execute its production run in parallel it complains of LINCS warning and > terminates at step 0. But on the contrary, it runs on the desktop > successfully. Kindly suggest something and please let me know if any more > information is required from my side. > > > Thanks!! > > > > Kind Regards, > Antara > > -- > Junior research fellow(project) > Systems biology group > CSIR-Institute of Genomics & Integrative Biology > South Campus > New Delhi - 110020 > M : +91-9717970040 > -- > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein
Dear Sir, I have used 1.8 rdd value. Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- On Sat, May 14, 2016 at 12:14 AM, subhadip das wrote: > Can you tell me of the constraint parameter u used and the corresponding > atom names > On 14 May 2016 00:11, "Tsjerk Wassenaar" wrote: > >> Hi Antara, >> >> What commands did you use? At least make sure you add -rdd 1.6 to the >> command line of mdrun, because the default value is too small for coarse >> grain simulations. >> >> Cheers, >> >> Tsjerk >> >> On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar > > >> >> wrote: >> >> > Dear users, >> > >> > I am trying to run a coarse grained simulation of a membrane protein in >> a >> > mixed lipid billayer using martini model 2.2. I have already performed >> all >> > the equilibration steps successfully on my desktop with GROMACS 5.1.0. >> > However, when i try to execute its production run in parallel(having >> > gromacs 5.1 version installed) it complains of LINCS warning and >> > terminates at step 0. But on the contrary, it runs on the desktop >> > successfully. Kindly suggest something and please let me know if any >> more >> > information is required from my side. >> > >> > >> > Thanks!! >> > >> > Kind Regards, >> > Antara >> > >> > -- >> > Junior research fellow(project) >> > Systems biology group >> > CSIR-Institute of Genomics & Integrative Biology >> > South Campus >> > New Delhi - 110020 >> > M : +91-9717970040 >> > -- >> > >> > >> > >> > On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar < >> antara.mazum...@igib.in >> > > >> > wrote: >> > >> > > Dear gromacs users, >> > > >> > > I am trying to run a coarse grained simulation of a membrane protein >> in a >> > > mixed lipid billayer using martini model. I have already performed all >> > the >> > > equilibration steps successfully on my desktop. However, when i try to >> > > execute its production run in parallel it complains of LINCS warning >> and >> > > terminates at step 0. But on the contrary, it runs on the desktop >> > > successfully. Kindly suggest something and please let me know if any >> more >> > > information is required from my side. >> > > >> > > >> > > Thanks!! >> > > >> > > >> > > >> > > Kind Regards, >> > > Antara >> > > >> > > -- >> > > Junior research fellow(project) >> > > Systems biology group >> > > CSIR-Institute of Genomics & Integrative Biology >> > > South Campus >> > > New Delhi - 110020 >> > > M : +91-9717970040 >> > > -- >> > > >> > > >> > > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL
Dear users, I am trying to run a coarse grained simulation of a membrane protein in a mixed lipid billayer using martini model 2.2. I have already performed all the equilibration steps successfully on my desktop with GROMACS 5.1.0. However, when i try to execute its production run in parallel(having gromacs 5.1 version installed) it complains of LINCS warning and terminates at step 0. The lincs warning error is coming from BB and SC1 atoms of one of the protein residues. But on the contrary, it runs on the desktop successfully. *My production run mdp file details are below :* . This is the MD.mdp file :ntegrator = md tinit= 0.0 dt = 0.020 nsteps = 25 nstxout = 2000 nstvout = 2000 nstfout = 2000 nstlog = 2000 nstenergy= 2000 nstxtcout= 2000 xtc_precision= 100 ns_type = grid pbc = xyz nstlist = 10 cutoff-scheme = Verlet rlist = 1.2 vdwtype = Cut-off vdw-modifier= none rvdw_switch = 1.0 rvdw= 1.2 coulombtype = pme rcoulomb= 1.2 tcoupl = v-rescale tc-grps = protein CHOL_POPC_DPSM_DPCE W_ION tau_t= 1.0 1.0 1.0 ref_t= 303.15 303.15 303.15 ; Pressure coupling: Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 5.0 5.0 compressibility = 3e-4 3e-4 ref_p= 1.0 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN: gen_vel = no refcoord_scaling = all *the command used for mdrun :* -deffnm MD -pin on -rdd 1.8 -np 16 I would also like to mention that i generated the initial structure of the system using CHARMM GUI MARTINI MAKER protein-membrane system option. I have followed the exact builder protocol for the equilibration and minimisation. Kindly suggest something! Thanks, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 55
duction tpr, i used the gro file from the last equilibration > > step(step6.6) The command used was : > >> > >> gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f > > MD.mdp -o MD.tpr > > > > That looks like it could be reasonable, but as with any equilibration you > > need to look at observables to judge that it's equilibrated. Their > builder > > should provide reasonable defaults, but you can't assume they're perfect, > > either. In particular, if the last equilibration ensemble doesn't match > the > > production ensemble, that could be the problem. > > > > Failing to pass the .cpt file to grompp -t after equilibration is a great > way to > do that. The production simulation is starting from some unpredictable > ensemble, without velocities, etc.. > > -Justin > > > Mark > > > > On Sat, May 14, 2016 at 5:10 PM Mark Abraham > > wrote: > > > >> Hi, > >> > >> On Sat, May 14, 2016 at 4:34 PM Antara mazumdar < > antara.mazum...@igib.in> > >> wrote: > >> > >>> Dear users, > >>> > >>> I am trying to run a coarse grained simulation of a membrane protein > in a > >>> mixed lipid billayer using martini model 2.2. I have already performed > all > >>> the equilibration steps successfully on my desktop with GROMACS 5.1.0. > >>> However, when i try to execute its production run in parallel(having > >>> gromacs 5.1 version installed) it complains of LINCS warning and > >>> terminates at step 0. The lincs warning error is coming from BB and SC1 > >>> atoms of one of the protein residues. > >>> > >> > >> There are lots of possible places to go wrong, including not making your > >> production .tpr based on the outputs of your equilibration. This seems > >> quite a likely possibility. > >> > >> You should also consider further equilibration - whether using Martini > or > >> not, it is sometimes necessary to use a small time step when relaxing > >> problem configurations. > >> > >> > >>> But on the contrary, it runs on the desktop successfully. *My > production > >>> run mdp file details are below :* > >>> > >>> > >>> . > >>> > >>> This is the MD.mdp file :ntegrator = md > >>> tinit= 0.0 > >>> dt = 0.020 > >>> nsteps = 25 > >>> > >>> nstxout = 2000 > >>> nstvout = 2000 > >>> nstfout = 2000 > >>> nstlog = 2000 > >>> nstenergy= 2000 > >>> nstxtcout= 2000 > >>> xtc_precision= 100 > >>> > >>> ns_type = grid > >>> pbc = xyz > >>> nstlist = 10 > >>> cutoff-scheme = Verlet > >>> rlist = 1.2 > >>> vdwtype = Cut-off > >>> vdw-modifier= none > >>> rvdw_switch = 1.0 > >>> rvdw= 1.2 > >>> coulombtype = pme > >>> rcoulomb= 1.2 > >>> > >>> tcoupl = v-rescale > >>> tc-grps = protein CHOL_POPC_DPSM_DPCE W_ION > >>> > >>> tau_t= 1.0 1.0 1.0 > >>> ref_t= 303.15 303.15 303.15 > >>> > >>> ; Pressure coupling: > >>> Pcoupl = berendsen > >>> Pcoupltype = semiisotropic > >>> tau_p= 5.0 5.0 > >>> compressibility = 3e-4 3e-4 > >>> ref_p= 1.0 1.0 > >>> ; GENERATE VELOCITIES FOR STARTUP RUN: > >>> gen_vel = no > >>> refcoord_scaling = all > >>> > >>> *the command used for mdrun :* > >>> > >>> -deffnm MD -pin on -rdd 1.8 -np 16 > >>> > >> > >> mdrun 5.1 won't accept -np, so I don't know what you are actually doing. > >> Please don't edit and filture things, copy and paste whole actual > things. > >> :-) > >> > >> Mark > >> > >> I would also like to mention that i generated the i
[gmx-users] Help required for calculation of protein coverage % wrt time
Dear gromacs users, I have a peripheral membrane protein which I have simulated using Charmm 36 in a mixed lipids bilayer. I want to calculate the percentage of protein in contact with membrane wrt time. I already have residue wise distances from membrane calculated. Can anyone suggest me how to go about it after this? Antara Mazumdar ISCB SC RSG-India Core Committee Member -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Help required for calculation of protein coverage % wrt time
Dear users, Is there any script available to calculate % occupancy of residues with respect to time? This in continuation with my previous query on percentage of protein in contact with membrane?? Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- On Thu, May 19, 2016 at 6:35 PM, Antara mazumdar wrote: > Dear gromacs users, > > I have a peripheral membrane protein which I have simulated using Charmm > 36 in a mixed lipids bilayer. I want to calculate the percentage of protein > in contact with membrane wrt time. I already have residue wise distances > from membrane calculated. > > Can anyone suggest me how to go about it after this? > > Antara Mazumdar > > ISCB SC RSG-India > > Core Committee Member > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] help required in calculating npme value for domain decomposition
Dear gromacs users, I need help in calculating the value of npme for the purpose of domain decomposition for my system of mixed lipid vesicles. Thanks!! Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr
Dear gromacs users, I was trying to dump structures from MD.trr using trjconv. The MD.trr has 0ns to 382ns of data. (i checked the MD.log file also). However, when i try to dump structures beyond 25ns, with the following command : *gmx trjconv mpi -f MD.trr -dump 27000.000 -dt 1000 -s MD.tpr -b 2.000* *it gives the following error :WARNING no output, last frame read at t=25290* I have also tried to check with gmxcheck but it only runs till 20ns. trjconv and or gmxcheck did not give any error with MD.xtc which was generated during the simulation. I require the MD.trr as i need velocity and force information for my analysis. Kindly suggest something!! Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] help required in plotting percentage of protein in contact with membrane vs time
Dear Gromacs users, I have a membrane protein simulation performed with gromacs 4.6. I have calculated the minimum distance of protein residues from upper leaflet of the lipid bilayer. I also have the time wise atom pair contacts as an output. The following command i used : g_mindist -f SYSTEM_FIT_SIM4_DT100.xtc -s MD_4_NOWATER.tpr -n ../index.ndx -d 0.7 -o atompair -on numcontact -od mindist.xvg The atom pair out output i got was as follow : .00e+00 2412281928 1.00e+02 1630266151 2.00e+02 1630266151 3.00e+02 2410284225 4.00e+02 2412284225 5.00e+02 2412284225 6.00e+02 2410284225 7.00e+02 2410284225 8.00e+02 2410284225 9.00e+02 2410284225 1.00e+03 2405284225 1.10e+03 2411281928 1.20e+03 2412284225 1.30e+03 2332285163 1.40e+03 2411284225 1.50e+03 2410284225 1.60e+03 1555264261 1.70e+03 1555264261 1.80e+03 1555264261 1.90e+03 1554266958 2.00e+03 2389266958 2.10e+03 2411285163 2.20e+03 2412285163 2.30e+03 2412285163 2.40e+03 2410285163 2.50e+03 2410285163 2.60e+03 2412285163 I now need to find out time wise percentage of protein covering the membrane. I want to know for instance, at time t=0ns, what is the protein coverage % and similarly for the entire trajectory i want to calculate this. Kindly suggest something!! Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr
Dear Sir, The MD.trr i expect to be having 382ns of data as is mentioned in the log file and MD.xtc that was generated alongwith MD.trr when the simulation ran has 382ns. However, MD.trr has problems in giving output beyond 25ns. Could it be corruption of frames or something? Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr
Dear Mark, I checked the file size , MD.trr is 3.2 Terabytes. It is a million atom system. What further could be done? Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system
Dear gromacs users, I am trying to calculate domain decomposition of a mixed lipid vesicle system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to run in parallel. I want to calculate the number of PME nodes per total number of nodes. However, i am not clear on how to calculate the value of nPME here. I would also mention that number of nodes that can be used need to be multiple of 16 and the value of minimum cell size is 1.8 nm. Can someone guide me in this regard? Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel
Dear Gromacs users, I was trying to do equilibration of a mixed lipid vesicle using gromacs 5.1 in parallel. My pbs script file details for this is the following : /home/lipi/openmpi164/bin/mpirun -np 48 /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm step6.2_equilibration -rdd 1.8 > test.dat However, the mdrun is terminated with the following two errors. *1)Cannot rename checkpoint file; maybe you are out of disk space?* i have checked the disk space, it still has terabytes of space left to be used. The folder where i am running it is hardly 45 MB. *2)mpirun noticed that process rank 10 with PID 62690 on node cn0013 exited on signal 11 (Segmentation fault).* Can anyone suggest me how to resolve it? Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel
Dear Users, I was trying to do equilibration of a mixed lipid vesicle using gromacs 5.1 in parallel using the below pasted pbs script : #!/bin/tcsh #PBS -l walltime=48:00:00 #PBS -N VES_new_16 #PBS -q workq #PBS -l select=1:ncpus=16:mpiprocs=16 #PBS -V # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR #export MPI_DEBUG=all #export MPI_IB_RAILS=2 #export MPI_DSM_DISTRIBUTE=1 #export MPI_VERBOSE=1 #export MPI_BUFS_THRESHOLD=1 #export MPI_BUFS_PER_PROC=1024 #export OMP_NUM_THREADS=1 #export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home1/gkpatra/gmp/lib module load intel-cluster-studio-2013 setenv OMP_NUM_THREADS 1 /home/lipi/openmpi164/bin/mpirun -np 16 /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm step6.2_equilibration -rdd 1.8 > test.dat This is generating multiple output and checkpoint files while its trying to run : #step6.2_equilibration.xtc.6# #step6.2_equilibration_step4400.cpt.1# #step6.2_equilibration.log.3# #step6.2_equilibration.log.5# #step6.2_equilibration.log.4# #step6.2_equilibration.log.2# step6.2_equilibration_prev.cpt #step6.2_equilibration.log.6# step6.2_equilibration.cpt #step6.2_equilibration.xtc.3# #step6.2_equilibration.xtc.5# #step6.2_equilibration.xtc.7# step6.2_equilibration.xtc When i check the log file to see the errors , it is showing the following : Step Time Lambda 00.00.0 Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 1.18159e+053.78079e+04 -8.79894e+06 -1.10782e+064.70754e+05 Flat-bottom posres PotentialKinetic En. Total Energy Temperature 4.65013e+06 -4.62990e+062.25820e+02 -4.62968e+066.73923e-02 Pressure (bar) -7.74545e+01 DD step 39 load imb.: force 22.2% Writing checkpoint, step 560 at Thu May 26 11:57:56 2016 --- Program gmx mdrun, VERSION 5.1.1 Source code file: /app/setups/gromacs-5.1.1/src/gromacs/gmxlib/checkpoint.cpp, line: 1670 File input/output error: Cannot rename checkpoint file; maybe you are out of disk space? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am not able to find the solution for it. What could be causing this? I have not been able to find help from HPC support available to us. Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel
Dear Mark, I will ask our HPC support team to check the MPI enabled version of gromacs then. Thank you for your suggestion. Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel
Dear Mark, Thanks for the suggestion. I will tell them that. Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Suggestion required for calculation of membrane contact sites and Lipid binding strength
Dear Gromacs users, Can anyone suggest me a way to find the membrane contact sites i.e. the lipids that are making contact with protein residues with respect to time from a membrane protein simulation? I have calculated the distance and contact of protein residues from upper leaflet atoms of bilayer already with a cutoff between 0.5 nm and 0.7 nm. I have the lipid numbers in the log file from g_hbond as well as g_dist. Should i be taking all these into account or a cutoff needs to be taken and can this be calculated wrt time? Secondly, has anyone found out the lipid binding strength from membrane protein simulations? Can we call the frequency of a protein residue to make a contact as its lipid binding strength? Here also, is there some way to find the binding strength wrt time? Thanks!! Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] query regarding coarse grained simulation of a peripheral membrane protein
Hi, How do i generate a topology file of a peripherally attached dimeric protein with a homogenous lipid bilayer using coarse grained approach? i have concatenated the coarse grained structure of lipids and protein prior to this. -- *Best,* *Antara* -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error in grompp : No such molecule type Protein
Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting "No such molecule type Protein" error. -- *Best,* *Antara* -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error in grompp : Something is wrong in the coordinate formatting of file system.gro
Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting *Something is wrong in the coordinate formatting of file system.gro* error. No such molecule type error does not come now. -- *Best,* *Antara* -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] URGENT query regarding pbc = no in grompp in membrane simulations
i want to simulate a system having membrane and proteins with pbc=no to allow surface effects. I use the following settings in my production mdp file : Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 ms dt = 0.002 ; 2 fs ; Output control ;trr file nstxout = 50; save coordinates every 1ns nstvout = 50; save velocities every 1ns nstenergy = 1 ; save energies every 20ps nstlog = 1 ; update log file every 20ps ;xtc file nstxtcout = 1 ; xtc compressed trajectory output every 20 ps ; Bond parameters constraint_algorithm = LINCS; holonomic constraints constraints= none ;ns-type= simple nstlist = 0 rlist = 0 coulombtype = Cut-off rcoulomb= 0.0 rvdw= 0 Periodic boundary conditions pbc = no; 3-D PBC ; Velocity generation gen_vel = YES ; Velocity generation is on comm_mode = ANGULAR however i get LINCS warning and also the log file says this : Your simulation settings would have triggered the efficient all-vs-all kernels in GROMACS 4.5, but these have not been implemented in GROMACS 4.6. Also, we can't use the accelerated SIMD kernels here because of an unfixed bug. The reference C kernels are correct, though, so we are proceeding by disabling all CPU architecture-specific (e.g. SSE2/SSE4/AVX) routines. If performance is important, please use GROMACS 4.5.7 or try cutoff-scheme = Verlet. kindly suggest something .. -- Best *,* Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.