[gmx-users] Error in Coarse Graining the atomistic trajectory
Dear Gromacs users, I am generating cg.gro using the below command, however the atoms considered as centre of mass in the output file is not the part of respective bead. seq 0 1999 | g_traj -f AA/trajpbc.xtc -s AA/topol.tpr -oxt traj_cg.xtc -n mapping.ndx -com -ng 2000 -b 2 I am not aware of how to troubleshoot the above problem. Any help will be highly appreciated. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Martini Website is not accessible
Okay, Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Mon, May 22, 2017 at 5:17 PM, Peter Kroon wrote: > Hi, > > > we are aware of it and will probably fix it later today. It's an update > gone wrong. > > > Peter > > > On 22-05-17 11:44, Anurag Dobhal wrote: > > Hello Gromacs users, > > > > This query is not related to typical gromacs error. I am unable to access > > the Martini Forcefield website (http://cgmartini.nl/) from the past few > > days. I just wanted to know if any of the gromacs users are aware of this > > issue ? am I opening the right website ? > > > > Thank you > > > > > > > > *Anurag Dobhal* > > *Graduate Student (Bioprocess Technology)* > > *Institute of Chemical Technology, Mumbai* > > > > > > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Martini Website is not accessible
Hello Gromacs users, This query is not related to typical gromacs error. I am unable to access the Martini Forcefield website (http://cgmartini.nl/) from the past few days. I just wanted to know if any of the gromacs users are aware of this issue ? am I opening the right website ? Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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 Umbrella sampling.
Dear Gromacs usrs, I am running a umbrella sampling simulation between two identical polymer chains in water using OPLS AA force field. My system does not have any charge. I have successfull generated the different configurations. While running the "gmx grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr" command to genetarte the .tpr file I got the following warning. " You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning " I am following the Umbrella sampling tutorial by Bevan Lab developed by Justin. I have used the npt_umbrella.mdp file given in the tutorial. Is is safe to use maxwarn in this case ? or is their any solution to overcome this warning ? Any help will be highly appreciated. Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Potential Energy is positive on minimizing the system
Thanks a lot! *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 9:10 PM, Justin Lemkul wrote: > > > On 2/23/17 9:07 AM, Anurag Dobhal wrote: > >> Dear Justin, >> >> I would like to know weather the parameters below are correct for NVT >> equilibiration whicle doig a simulation in vaccum ? >> >> define = -DPOSRES ; position restrain the protein >> > > If you don't have solvent, there's no reason to restrain anything. > Normally one restrains the solute to allow the solvent to relax around it. > Here, this serves no purpose. > > ; Run parameters >> integrator = md ; leap-frog integrator >> nsteps = 5 ; 2 * 5 = 100 ps >> dt = 0.002 ; 2 fs >> ; Output control >> nstxout = 100 ; save coordinates every 0.2 ps >> nstvout = 100 ; save velocities every 0.2 ps >> nstenergy = 100 ; save energies every 0.2 ps >> nstlog = 100 ; update log file every 0.2 ps >> ; Bond parameters >> continuation = no ; first dynamics run >> constraint_algorithm = lincs ; holonomic constraints >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained >> lincs_iter = 1 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> ; Neighborsearching >> ns_type = simple ; search neighboring grid cells >> > > Note you also need cutoff-scheme = group here. > > nstlist = 0 ; 10 fs >> rlist = 0.0 ; short-range neighborlist cutoff (in nm) >> rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm) >> rvdw = 0.0 ; short-range van der Waals cutoff (in nm) >> ; Electrostatics >> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics >> > > As I said before, you can't use PME (grompp will fail anyway, because you > can't have PME without PBC). Use a plain cutoff. > > pme_order = 0 ; cubic interpolation >> fourierspacing = 0.0 ; grid spacing for FFT >> ; Temperature coupling is on >> tcoupl = V-rescale ; modified Berendsen thermostat >> tc-grps = Other ; two coupling groups - more accurate >> tau_t = 0.1 ; time constant, in ps >> ref_t = 300 ; reference temperature, one for each group, in K >> ; Pressure coupling is off >> pcoupl = no ; no pressure coupling in NVT >> ; Periodic boundary conditions >> pbc = no ; 3-D PBC >> ; Dispersion correction >> DispCorr = EnerPres ; account for cut-off vdW scheme >> > > Dispersion correction is also not applicable. > > -Justin > > ; Velocity generation >> gen_vel = yes ; assign velocities from Maxwell distribution >> gen_temp = 300 ; temperature for Maxwell distribution >> gen_seed = -1 ; generate a random seed >> >> Thank You >> >> >> >> >> *Anurag Dobhal* >> *Graduate Student (Bioprocess Technology)* >> *Institute of Chemical Technology, Mumbai* >> *Contact: +91 8898486877* >> >> >> On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal < >> anurag.dob...@nano-medicine.co.in> wrote: >> >> Thank you ! >>> >>> >>> >>> >>> *Anurag Dobhal* >>> *Graduate Student (Bioprocess Technology)* >>> *Institute of Chemical Technology, Mumbai* >>> *Contact: +91 8898486877* >>> >>> >>> >>> On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul wrote: >>> >>> >>>> >>>> On 2/23/17 8:29 AM, Anurag Dobhal wrote: >>>> >>>> Thank you. Should I not use PME and PBC while performing simulations in >>>>> Vaccum ? >>>>> >>>>> >>>>> No, you should not. Use no PBC and infinite cutoffs (all cutoffs set >>>> to >>>> zero) to mimic vacuum conditions. Otherwise you're simulating some >>>> type of >>>> diffusely occupied crystal environment. >>>> >>>> >>>> -Justin >>>> >>>> -- >>>> == >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>> >>>> Department of Pharmaceutical Sciences >>>> School of Pharmacy >>>> Health Sciences Facility II, Room 629 >>>> University of Maryland, Baltimore >>>> 20 Penn St. >>>> Baltimore, MD 21201 >>>> >>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>> http://mackerell.umaryland.edu/~jalemkul >>>> >
Re: [gmx-users] Potential Energy is positive on minimizing the system
Dear Justin, I would like to know weather the parameters below are correct for NVT equilibiration whicle doig a simulation in vaccum ? define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm) rvdw = 0.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 0 ; cubic interpolation fourierspacing = 0.0 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Other ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = no ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Thank you ! > > > > > *Anurag Dobhal* > *Graduate Student (Bioprocess Technology)* > *Institute of Chemical Technology, Mumbai* > *Contact: +91 8898486877* > > > On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul wrote: > >> >> >> On 2/23/17 8:29 AM, Anurag Dobhal wrote: >> >>> Thank you. Should I not use PME and PBC while performing simulations in >>> Vaccum ? >>> >>> >> No, you should not. Use no PBC and infinite cutoffs (all cutoffs set to >> zero) to mimic vacuum conditions. Otherwise you're simulating some type of >> diffusely occupied crystal environment. >> >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> -- >> 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. >> > > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Potential Energy is positive on minimizing the system
Thank you ! *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul wrote: > > > On 2/23/17 8:29 AM, Anurag Dobhal wrote: > >> Thank you. Should I not use PME and PBC while performing simulations in >> Vaccum ? >> >> > No, you should not. Use no PBC and infinite cutoffs (all cutoffs set to > zero) to mimic vacuum conditions. Otherwise you're simulating some type of > diffusely occupied crystal environment. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Potential Energy is positive on minimizing the system
Thank you. Should I not use PME and PBC while performing simulations in Vaccum ? -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Potential Energy is positive on minimizing the system
Dear gromacs users, I am Simulating a polymer chain having 20 monomer units. I am doing the simulation in the vaccum (I am not solvating the system). The total charge in my polymer chain is +9 and I am not nutrealizing the system as I was suggested earlier that if we are simulating a system in a vaccum we can continue without neutralizing the system (https://www.mail-archive.com/ gromacs.org_gmx-users@maillist.sys.kth.se/msg23520.html). Now when I am minimizing my system I am not getting negative potential energy (Potential Energy = 4.5656064e+03). I am using gromacs Version 4.6.5 and the parameters of the minim.mdp are below ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Any help will be appreciated. Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Potential Energy is positive on minimizing the system
Dear gromacs users, I am Simulating a polymer chain having 20 monomer units. I am doing the simulation in the vaccum (I am not solvating the system). The total charge in my polymer chain is +9 and I am not nutrealizing the system as I was suggested earlier that if we are simulating a system in a vaccum we can continue without neutralizing the system ( https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg23520.html ). Now when I am minimizing my system I am not getting negative potential energy (Potential Energy = 4.5656064e+03). I am using gromacs Version 4.6.5 and the parameters of the minim.mdp are below ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Any help will be appreciated. Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Neutralization of the non solvated system
Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Thu, Dec 22, 2016 at 6:26 PM, Justin Lemkul wrote: > > > On 12/22/16 5:24 AM, Anurag Dobhal wrote: > >> Dear Gromacs users, >> >> I am simulating a polyemer chain having positive charge. I am running the >> simulation without any solvent, in this sitiuation how can I neutralize my >> system ? >> >> > You don't. There's nothing wrong with simulating a charged species in > vacuo. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Neutralization of the non solvated system
Dear Gromacs users, I am simulating a polyemer chain having positive charge. I am running the simulation without any solvent, in this sitiuation how can I neutralize my system ? Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Invalid order for directive molecules
Dear Gromacs users, I am running a coarse grained simulation of a polymer using mirtini force field. I have already made the .ito and .top file but i m getting the following error. Fatal error: Syntax error - File ppp.top, line 24 Last line read: '[ molecules ]' Invalid order for directive molecules How should I write my topol.top file below are the contents of topol.top ; Include forcefield parameters #include "./oplsaa.ff/martini_v2.2.itp" #include "./oplsaa.ff/plgacg.itp" [ molecules ] ; Compound#mols PLGA 1 Looking forward for your help. Thanks and Regards *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding tc-grps
Thank you Justin and Peter for the valuable inputs. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Thu, Sep 29, 2016 at 8:25 PM, Peter Kroon wrote: > Hi, > > please see http://www.gromacs.org/Documentation/Terminology/Thermostats > > The number of molecule types (what you call groups?) in your .top file > are not relevant for the number of tc groups you make. > > You need to make sure your system obeys a boltzmann distribution (or > maxwell? I'm not sure). In principle a single temperature coupling group > is always enough, but the exchange of thermal energy between i.e. a > protein and the surrouding solvent may not be efficient enough to make > sure that this is true. In such a case people use two (or more) > temperature coupling groups. > > To sum up: your system as a whole needs to obey a certain distribution > of kinetic energy. In addition, every "subsystem" (i.e. protein or > solvent or any combination thereoff) needs to obey such a distribution > as well. > > In your case, I think a single tc group (System) should be enough. > > > HTH, > > Peter > > > On 29-09-16 16:31, Anurag Dobhal wrote: > > Dear Gromacs users, > > > > I am simulating a polymer chain without any solvent using OPLS AA force > > field, how many tc-grps should I put in the .mdp file ? as there is only > > one 1 group in the topol.top file. > > > > Thank You > > > > > > > > *Anurag Dobhal* > > *Graduate Student (Bioprocess Technology)* > > *Institute of Chemical Technology, Mumbai* > > > > > > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding tc-grps
Thank you Justin for the reply. Actully when I am simulating the polymer in solvent (Water) the system is getting properly simulated in NVT,NPT equilibration and production run steps. But when the same system is simulated without water ( I kept only one tc-grp in the .mdp file) the system is stoping, showing error of segmentation fault. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Thu, Sep 29, 2016 at 8:26 PM, Justin Lemkul wrote: > > > On 9/29/16 10:31 AM, Anurag Dobhal wrote: > >> Dear Gromacs users, >> >> I am simulating a polymer chain without any solvent using OPLS AA force >> field, how many tc-grps should I put in the .mdp file ? as there is only >> one 1 group in the topol.top file. >> >> > Then what option do you have? If you've got a polymer and nothing else, > there's no way to create separate tc-grps, anyway. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding tc-grps
Dear Gromacs users, I am simulating a polymer chain without any solvent using OPLS AA force field, how many tc-grps should I put in the .mdp file ? as there is only one 1 group in the topol.top file. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] changing the location of a molecule in a box
Dear Gromacs users, I am working on a biphasic system where I have taken chloroform and water as two solvents. I want to locate my protien at the center of the box such that half of the protien is solvated in water and other half in the chloroform. How can I acheive the desired placement of the protien. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* On Fri, Sep 9, 2016 at 4:24 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear Gromacs users, > > I am working on a biphasic system where I have taken chloroform and water > as two solvents. I want to locate my protien at the center of the box such > that half of the protien is solvated in water and other half in the water. > > How can I acheive the desired placement of the protien. > > Thank You > > > > *Anurag Dobhal* > *Graduate Student (Bioprocess Technology)* > > > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] changing the location of a molecule in a box
Dear Gromacs users, I am working on a biphasic system where I have taken chloroform and water as two solvents. I want to locate my protien at the center of the box such that half of the protien is solvated in water and other half in the water. How can I acheive the desired placement of the protien. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Parameters file for CHARMM 27 Force Field
Dear Gromacs users, I am writing CHARMM27 parameters for a new molecule. Where can I get a parameter file for the CHARMM27 ? where all parameters for all the atoms are available similar file for OPLS/AA force filed can be found in below link. https://drive.google.com/open?id=0B011-Vz79yKJWFgwYVN3cUJHSUE Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Energy minimization has stopped
Thanks a lot Justinn and Mark for the valuable suggestions. I will start over again by choosing a force field which is suitable for the RNA molecules. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:55 PM, Justin Lemkul wrote: > > > On 6/23/16 7:17 AM, Anurag Dobhal wrote: > >> Dear Justin, >> >> The main aim of the study is to study the interaction between a polymer >> (chitosan) and RNA molecules by simulating them togather. I have already >> successfully simulated my polymer system using OPLS AA force field. >> >> To simulate them together I need to write the OPLS AA parameters for RNA >> molecules. I was suggested (Link Below) earlier that I can take the >> charges >> from any other forcefield. >> >> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) >> >> please enlight me where I am going wrong. >> >> > I think you misunderstood what I said in that thread. > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html > > "You should find force field parameters specifically for the base from > published literature or from another force field." > > This means: find a force field that has parametrized the species you need > and use it. This does not mean: hack together something from "any other > force field" you like and try to make it OPLS-AA. You did not say before > that you were dealing with a complex system like this. You just said your > guanine charges didn't add up. So I addressed that problem. > > Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an > invalid approach. > > Pick a force field. Use that force field. Do not try to kludge together > some hybrid entity. Force fields are designed to be internally > self-consistent. If you do not have a proper balance of interactions, you > are not doing a useful simulation. You are generating random numbers. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Energy minimization has stopped
Dear Justin, The main aim of the study is to study the interaction between a polymer (chitosan) and RNA molecules by simulating them togather. I have already successfully simulated my polymer system using OPLS AA force field. To simulate them together I need to write the OPLS AA parameters for RNA molecules. I was suggested (Link Below) earlier that I can take the charges from any other forcefield. (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) please enlight me where I am going wrong. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul wrote: > > > On 6/23/16 7:00 AM, Anurag Dobhal wrote: > >> I am using OPLS AA force field. parameters (charges) for the atoms are >> taken from the charmm27 force field. >> >> > So, by using some hybridized force field, you can't successfully minimize > a structure. That should tell you something. Why are you trying to do > this, and what leads you to believe that some hybrid OPLS/CHARMM > combination is even sensible? You can't just mix the charges from one > force field with another to create some kind of Frankenforcefield. > > Recent RNA force fields like CHARMM36 and recent AMBER updates are highly > optimized for RNA simulations. > > -Justin > > >> >> >> *Anurag Dobhal* >> *Graduate Student (Bioprocess Technology)* >> *Institute of Chemical Technology, Mumbai* >> *Contact: +91 8898486877* >> >> >> >> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote: >> >> >>> >>> On 6/23/16 6:44 AM, Justin Lemkul wrote: >>> >>> >>>> >>>> On 6/23/16 6:35 AM, Anurag Dobhal wrote: >>>> >>>> Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force >>>>> field. I have written parameters using CHARMM27 force field for RNA >>>>> molecules. >>>>> >>>>> >>>>> What does this mean? Are you using OPLS-AA or CHARMM27? >>>> >>>> >>>> Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly >>> superior for RNA. >>> >>> -Justin >>> >>> >>> Minimising the molecule by invoking mdrun gives me the follwoing error. >>> >>>> >>>>> Energy minimization has stopped, but the forces have not converged to >>>>> the >>>>> requested precision Fmax < 1000 (which may not be possible for your >>>>> system). >>>>> It stopped because the algorithm tried to make a new step whose size >>>>> was >>>>> too >>>>> small, or there was no change in the energy since last step. Either >>>>> way, >>>>> we >>>>> regard the minimization as converged to within the available machine >>>>> precision, given your starting configuration and EM parameters. >>>>> >>>>> Double precision normally gives you higher accuracy, but this is often >>>>> not >>>>> needed for preparing to run molecular dynamics. >>>>> You might need to increase your constraint accuracy, or turn >>>>> off constraints altogether (set constraints = none in mdp file) >>>>> >>>>> >>>>> >>>>> - >>>>> >>>>> The contents of the .mdp file are the following >>>>> >>>>> ; minim.mdp - used as input into grompp to generate em.tpr >>>>> integrator = steep ; Algorithm (steep = steepest descent minimization) >>>>> emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 >>>>> kJ/mol/nm >>>>> emstep = 0.01 ; Energy step size >>>>> nsteps = 5 ; Maximum number of (minimization) steps to perform >>>>> >>>>> ; Parameters describing how to find the neighbors of each atom and how >>>>> to >>>>> calculate the interactions >>>>> nstlist= 1; Frequency to update the neighbor list and long >>>>> range >>>>> forces >>>>> cutoff-scheme = Verlet >>>>> ns_type= grid ; Method to determine neighbor list (simple, grid) >>>>> coulombtype= PME ; Treatment of long range
Re: [gmx-users] Energy minimization has stopped
I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote: > > > On 6/23/16 6:44 AM, Justin Lemkul wrote: > >> >> >> On 6/23/16 6:35 AM, Anurag Dobhal wrote: >> >>> Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force >>> field. I have written parameters using CHARMM27 force field for RNA >>> molecules. >>> >>> >> What does this mean? Are you using OPLS-AA or CHARMM27? >> >> > Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly > superior for RNA. > > -Justin > > > Minimising the molecule by invoking mdrun gives me the follwoing error. >>> >>> Energy minimization has stopped, but the forces have not converged to the >>> requested precision Fmax < 1000 (which may not be possible for your >>> system). >>> It stopped because the algorithm tried to make a new step whose size was >>> too >>> small, or there was no change in the energy since last step. Either way, >>> we >>> regard the minimization as converged to within the available machine >>> precision, given your starting configuration and EM parameters. >>> >>> Double precision normally gives you higher accuracy, but this is often >>> not >>> needed for preparing to run molecular dynamics. >>> You might need to increase your constraint accuracy, or turn >>> off constraints altogether (set constraints = none in mdp file) >>> >>> >>> - >>> >>> The contents of the .mdp file are the following >>> >>> ; minim.mdp - used as input into grompp to generate em.tpr >>> integrator = steep ; Algorithm (steep = steepest descent minimization) >>> emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 >>> kJ/mol/nm >>> emstep = 0.01 ; Energy step size >>> nsteps = 5 ; Maximum number of (minimization) steps to perform >>> >>> ; Parameters describing how to find the neighbors of each atom and how to >>> calculate the interactions >>> nstlist= 1; Frequency to update the neighbor list and long range >>> forces >>> cutoff-scheme = Verlet >>> ns_type= grid ; Method to determine neighbor list (simple, grid) >>> coulombtype= PME ; Treatment of long range electrostatic interactions >>> rcoulomb= 1.0 ; Short-range electrostatic cut-off >>> rvdw= 1.0 ; Short-range Van der Waals cut-off >>> pbc= xyz ; Periodic Boundary Conditions (yes/no) >>> >>> any suggestions ? >>> >>> >> >> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision >> >> >> mdrun prints which atom is feeling the maximum force, so that's a good >> place to >> start looking to see if there is an actual problem. >> >> -Justin >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Energy minimization has stopped
Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) - The contents of the .mdp file are the following ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid ; Method to determine neighbor list (simple, grid) coulombtype= PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) any suggestions ? *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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: Duplicate line found in or between hackblock and rtp entries
Dear Gromacs Users, I Simulated a Nucleotide pair using OPLS AA force field. while running " gmx pdb2gmx" I am getting the following warning. WARNING: Duplicate line found in or between hackblock and rtp entries How to address this warning ? Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Total Charge on Guanine molecule by OPLS AA force field is negative
Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Fri, Jun 17, 2016 at 5:02 PM, Justin Lemkul wrote: > > > On 6/17/16 6:26 AM, Anurag Dobhal wrote: > >> Dear Justin, >> >> I have already added the H to the guanine molecule striped from the >> nucleotide. >> The charges given in the ffnonbonded.itp for all the atoms of guanine >> (Including the H on N9) do not add to zero. >> >> > As I said, those charges mean nothing. You should find force field > parameters specifically for the base from published literature or from > another force field. AMBER and CHARMM are much better choices than OPLS-AA > for nucleic acids and their components, anyway. CHARMM has a topology for > all bases as part of the stock force field. > > -Justin > > >> >> >> >> >> *Anurag Dobhal* >> *Graduate Student (Bioprocess Technology)* >> *Institute of Chemical Technology, Mumbai* >> *Contact: +91 8898486877* >> >> >> >> On Fri, Jun 17, 2016 at 3:36 PM, Justin Lemkul wrote: >> >> >>> >>> On 6/17/16 4:42 AM, Anurag Dobhal wrote: >>> >>> Dear Gromacs users, >>>> >>>> I want to simulate Guanine ( a nitrogenous base) molecules in water >>>> using >>>> OPLS AA force field. >>>> >>>> I used the "opls aa" parameters from atomtypes.atp >>>> ((JACS,113,2810(1991)). >>>> on calculating the total charge of one molecule it comes to a negative >>>> value. >>>> >>>> >>> The .atp file has no charges. The charges found in ffnonbonded.itp also >>> mean nothing. >>> >>> dose it means that guanine has negative charge ? >>> >>>> >>>> >>> Not as just the base. The nucleotide form is of course anionic. >>> >>> should I continue with thae same parameters or change them to bring the >>> >>>> total charge of the molecule to zero. >>>> >>>> >>>> You should be sure you have a proper model with a reliable source of >>> parameters. Stripping the base out of a nucleotide also requires the >>> introduction of an H to fill the valence at the glycosidic linkage. >>> Charges may differ as a result of such a change. >>> >>> -Justin >>> >>> Thank You for your help >>> >>>> >>>> >>>> *Anurag Dobhal* >>>> *Graduate Student (Bioprocess Technology)* >>>> *Institute of Chemical Technology, Mumbai* >>>> >>>> >>>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> 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. >>> >>> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Total Charge on Guanine molecule by OPLS AA force field is negative
Dear Justin, I have already added the H to the guanine molecule striped from the nucleotide. The charges given in the ffnonbonded.itp for all the atoms of guanine (Including the H on N9) do not add to zero. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Fri, Jun 17, 2016 at 3:36 PM, Justin Lemkul wrote: > > > On 6/17/16 4:42 AM, Anurag Dobhal wrote: > >> Dear Gromacs users, >> >> I want to simulate Guanine ( a nitrogenous base) molecules in water using >> OPLS AA force field. >> >> I used the "opls aa" parameters from atomtypes.atp >> ((JACS,113,2810(1991)). >> on calculating the total charge of one molecule it comes to a negative >> value. >> > > The .atp file has no charges. The charges found in ffnonbonded.itp also > mean nothing. > > dose it means that guanine has negative charge ? >> > > Not as just the base. The nucleotide form is of course anionic. > > should I continue with thae same parameters or change them to bring the >> total charge of the molecule to zero. >> >> > You should be sure you have a proper model with a reliable source of > parameters. Stripping the base out of a nucleotide also requires the > introduction of an H to fill the valence at the glycosidic linkage. > Charges may differ as a result of such a change. > > -Justin > > Thank You for your help >> >> >> *Anurag Dobhal* >> *Graduate Student (Bioprocess Technology)* >> *Institute of Chemical Technology, Mumbai* >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Total Charge on Guanine molecule by OPLS AA force field is negative
Dear Gromacs users, I want to simulate Guanine ( a nitrogenous base) molecules in water using OPLS AA force field. I used the "opls aa" parameters from atomtypes.atp ((JACS,113,2810(1991)). on calculating the total charge of one molecule it comes to a negative value. dose it means that guanine has negative charge ? should I continue with thae same parameters or change them to bring the total charge of the molecule to zero. Thank You for your help *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Grompp error
Thanks a lot for your insight. I will redefine them. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Mon, May 30, 2016 at 8:26 PM, Justin Lemkul wrote: > > > On 5/30/16 10:55 AM, Anurag Dobhal wrote: > >> Thanks a lot for your reply. >> >> I have set tc-groups as >> >> >> tc-grps = Other acetone ; two coupling groups - more accurate >> tau_t = 0.1 0.1 ; time constant, in ps >> ref_t = 300 300 ; reference temperature, one for each >> >> >> > Then you can't rely on such groups to be correct. Other and acetone > overlap. Define appropriate groups. > > -Justin > > >> >> *Anurag Dobhal* >> *Graduate Student (Bioprocess Technology)* >> *Institute of Chemical Technology, Mumbai* >> *Contact: +91 8898486877* >> >> >> >> On Mon, May 30, 2016 at 8:18 PM, Justin Lemkul wrote: >> >> >>> >>> On 5/30/16 10:40 AM, Anurag Dobhal wrote: >>> >>> Dear Gromacs users >>>> >>>> I am solvating my molecule ( a ploymer chain, having 78 atoms) in >>>> Propan-2-one >>>> [ molecules] = acetone. I have already updated [ molecules ] section in >>>> the topology file (topol.top) after the solvation step. >>>> >>>> after the sucessful energy minimization step, while runing grompp I am >>>> geting an error, >>>> >>>> " Excluding 3 bonded neighbours molecule type 'Other' >>>> turning all bonds into constraints... >>>> Excluding 3 bonded neighbours molecule type 'acetone' >>>> turning all bonds into constraints... >>>> Setting gen_seed to 3080450167 >>>> Velocities were taken from a Maxwell distribution at 300 K >>>> Removing all charge groups because cutoff-scheme=Verlet >>>> >>>> Fatal error: >>>> Atom 79 in multiple T-Coupling groups (1 and 2) " >>>> >>>> The error means that T-coupling is treating both the polymer (other) and >>>> solvent (acetone) as other molecules. >>>> How can I rectify the error ? >>>> >>>> >>>> You haven't shown us what you've set as tc-grps but there is clearly >>> redundancy between whatever those groups are. If you have multiple >>> groups, >>> you need to ensure that they are defined correctly, using index groups as >>> needed. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> 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. >>> >>> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Grompp error
Thanks a lot for your reply. I have set tc-groups as tc-grps = Other acetone ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Mon, May 30, 2016 at 8:18 PM, Justin Lemkul wrote: > > > On 5/30/16 10:40 AM, Anurag Dobhal wrote: > >> Dear Gromacs users >> >> I am solvating my molecule ( a ploymer chain, having 78 atoms) in >> Propan-2-one >> [ molecules] = acetone. I have already updated [ molecules ] section in >> the topology file (topol.top) after the solvation step. >> >> after the sucessful energy minimization step, while runing grompp I am >> geting an error, >> >> " Excluding 3 bonded neighbours molecule type 'Other' >> turning all bonds into constraints... >> Excluding 3 bonded neighbours molecule type 'acetone' >> turning all bonds into constraints... >> Setting gen_seed to 3080450167 >> Velocities were taken from a Maxwell distribution at 300 K >> Removing all charge groups because cutoff-scheme=Verlet >> >> Fatal error: >> Atom 79 in multiple T-Coupling groups (1 and 2) " >> >> The error means that T-coupling is treating both the polymer (other) and >> solvent (acetone) as other molecules. >> How can I rectify the error ? >> >> > You haven't shown us what you've set as tc-grps but there is clearly > redundancy between whatever those groups are. If you have multiple groups, > you need to ensure that they are defined correctly, using index groups as > needed. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Grompp error
Dear Gromacs users I am solvating my molecule ( a ploymer chain, having 78 atoms) in Propan-2-one [ molecules] = acetone. I have already updated [ molecules ] section in the topology file (topol.top) after the solvation step. after the sucessful energy minimization step, while runing grompp I am geting an error, " Excluding 3 bonded neighbours molecule type 'Other' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'acetone' turning all bonds into constraints... Setting gen_seed to 3080450167 Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet Fatal error: Atom 79 in multiple T-Coupling groups (1 and 2) " The error means that T-coupling is treating both the polymer (other) and solvent (acetone) as other molecules. How can I rectify the error ? *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] uninstall gromacs 5.0
Thank a lot Mark and Sun for your valuable suggestions. The problem is solved. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Mon, May 23, 2016 at 10:43 PM, sun wrote: > I am sorry for so many e-mails but check this link: > > http://installion.co.uk/ubuntu/vivid/universe/g/gromacs/uninstall/index.html > > Sent from my iPhone > > > On 23-May-2016, at 9:49 pm, Mark Abraham > wrote: > > > > Hi, > > > > sun, that is not the name of any apt-supported GROMACS package that I > know > > of... > > > > Mark > > > >> On Mon, May 23, 2016 at 6:17 PM sun wrote: > >> > >> sudo apt-get uninstall Gromacs-5.0 > >> > >> > >> > >> Sent from my iPhone > >> > >>>> On 23-May-2016, at 6:51 pm, Anurag Dobhal < > >>> anurag.dob...@nano-medicine.co.in> wrote: > >>> > >>> Dear Users: > >>> > >>> I want to uninstall gromacs 5.0 and replace it with gromacs 5.1. > >>> The link provided in the gromacs website (Removing a GROMACS > >> installation) > >>> does not give any solution with the same. > >>> > >>> how can i uninstall gromacs 5.0 ?? > >>> > >>> > >>> Thanks in advance. > >>> > >>> Anurag Dobhal > >>> > >>> -- > >>> > >>> > >>> *DISCLAIMER:* > >>> > >>> *This communication is intended only for the person or entity to which > it > >>> is addressed and may contain confidential and / or privileged material. > >> Any > >>> review, retransmission, dissemination or other use is prohibited. If > you > >>> have received this in error, please contact the sender and delete this > >>> material from your computer. Any comments or statements made herein do > >> not > >>> necessarily reflect those of Nanomedicine Research Group. Before > opening > >>> the email or accessing any attachments, please check and scan for > virus.* > >>> -- > >>> 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. > > -- > > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] uninstall gromacs 5.0
Dear Users: I want to uninstall gromacs 5.0 and replace it with gromacs 5.1. The link provided in the gromacs website (Removing a GROMACS installation) does not give any solution with the same. how can i uninstall gromacs 5.0 ?? Thanks in advance. Anurag Dobhal -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Grompp Error No default Ryckaert-Bell. types
Dear gromacs users. I am simulating a molecule in opls-aa force field. While running energy minimization I did get the error "No default Ryckaert-Bell. types". I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO) has No default Ryckaert-Bell. types. but on checking ffbonded.itp I found that this dihedral is already present as in line 1346 as. C CT OH HO 3 -0.44350 3.83255 0.72801 -4.11705 0.0 0.0 ; anybody have any idea what is the reason for this error ??? *Anurag DobhalJunior Research fellowSupervisor: Dr. Ratnesh D. JainDepartment of chemical engineeringInstitute of Chemical Technology400019, +91 8898486877* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Grompp error "No default Ryckaert-Bell. types"
Hello all How can I address the "No default Ryckaert-Bell. types error". The error is also in between the atoms which are not bonded with each other. Thank you -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Fatal error: Atom type Zn2+ (residue ZN) not found in atomtype database
Dear all I am running pdb2gmx to creat the topology file of my structure, But I did get the error Fatal error: Atom type Zn2+ (residue ZN) not found in atomtype database Although my .pdb file does not contain Atom type Zn2+ (residue ZN) *Anurag DobhalJuniour Research fellowSupervisor: Dr. Ratnesh D. JainDepartment of chemical engineeringInsttute of Chemical Technology400019, +91 8898486877* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
Thank a lot Justin for your help and time. Thank you On Fri, Oct 3, 2014 at 5:21 PM, Justin Lemkul wrote: > > > On 10/3/14 7:48 AM, Anurag Dobhal wrote: > >> How to iteration the system 26 times. I am unable to understand that part. >> >> please explain how to do it. >> >> > Please have a bit of patience when waiting for a reply rather than > spamming the list every hour with follow-ups. It took quite a while for me > to type my last reply (just sent) and the level of detail is quite > extensive. I do not have the ability to instantly answer every message; > please understand that I have a lot of other things that I do each day ;) > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
How to iteration the system 26 times. I am unable to understand that part. please explain how to do it. Thank you On Fri, Oct 3, 2014 at 3:51 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > hello Justin thanks for your reply. > > I am unable to understand how to proceed in this tutorial. I am working on > it from many days but I am unable to do. > > I have understood till the step. > > perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat > > this is the result which I got. > > Area per protein: 2 nm^2 > Area per lipid: 10.4716089904762 nm^2 > > Area per protein, upper half: 1.75 nm^2 > Area per lipid, upper leaflet : 10.475577244 nm^2 > > Area per protein, lower half: 2 nm^2 > Area per lipid, lower leaflet : 10.4716089904762 nm^2 > > Writing Area per lipid... > Done! > > > and the minimization step after that. I get the confout.gro file. > > > I am confused how to continue from the step > > "perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 > area_shrink1.dat" > > how many times do we need to run this command, nd with what changes > > and how to solvate the system ( which file ) and what will be the command ??? > > looking for your kind reply. > > please help. > > Thank you > > > > On Thu, Oct 2, 2014 at 10:22 PM, Justin Lemkul wrote: > >> >> >> On 10/2/14 12:51 PM, Anurag Dobhal wrote: >> >>> how will I get to know that the system have shrunken enough, and which >>> file >>> I need to solvate. >>> >>> >> This is stated in the tutorial. >> >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> -- >> 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. >> > > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
hello Justin thanks for your reply. I am unable to understand how to proceed in this tutorial. I am working on it from many days but I am unable to do. I have understood till the step. perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat this is the result which I got. Area per protein: 2 nm^2 Area per lipid: 10.4716089904762 nm^2 Area per protein, upper half: 1.75 nm^2 Area per lipid, upper leaflet : 10.475577244 nm^2 Area per protein, lower half: 2 nm^2 Area per lipid, lower leaflet : 10.4716089904762 nm^2 Writing Area per lipid... Done! and the minimization step after that. I get the confout.gro file. I am confused how to continue from the step "perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat" how many times do we need to run this command, nd with what changes and how to solvate the system ( which file ) and what will be the command ??? looking for your kind reply. please help. Thank you On Thu, Oct 2, 2014 at 10:22 PM, Justin Lemkul wrote: > > > On 10/2/14 12:51 PM, Anurag Dobhal wrote: > >> how will I get to know that the system have shrunken enough, and which >> file >> I need to solvate. >> >> > This is stated in the tutorial. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
how will I get to know that the system have shrunken enough, and which file I need to solvate. On Thu, Oct 2, 2014 at 9:16 PM, Justin Lemkul wrote: > > > On 10/2/14 8:50 AM, Anurag Dobhal wrote: > >> Thanks Justin >> >> I m running the command >> >> " mdrun -s em.tpr " and I did get the confout.gro file as output. >> >> after that I am running the command >> >> " perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 >> area_shrink1.dat " >> and then again the energy minimization command. >> >> " mdrun -s em.tpr" >> >> After that I am solvating the system. >> I did put a local copy of vdwradii.dat in my working directorie and >> change >> the value of C from 0.15 to 0.375. >> >> >> I am solvating my system by the command >> >> " genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p >> topol.top " >> >> after that I am adding the ions in the system by the command >> >> " grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr" >> >> But now I am getting an error >> >> number of coordinates in coordinate file (system_solv.gro, 8218) >> does not match topology (topol.top, 1956) >> >> >> can you please help what caused this error. >> >> > Don't solvate the intermediate steps. It makes no physical sense. Only > solvate when you have shrunk the system to an appropriate size based on > APL. Regardless, the number of atoms in the system is way too small to be > correct for the tutorial system. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
Thanks Justin I m running the command " mdrun -s em.tpr " and I did get the confout.gro file as output. after that I am running the command " perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat " and then again the energy minimization command. " mdrun -s em.tpr " After that I am solvating the system. I did put a local copy of vdwradii.dat in my working directorie and change the value of C from 0.15 to 0.375. I am solvating my system by the command " genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p topol.top " after that I am adding the ions in the system by the command " grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr " But now I am getting an error number of coordinates in coordinate file (system_solv.gro, 8218) does not match topology (topol.top, 1956) can you please help what caused this error. Thanking you On Tue, Sep 30, 2014 at 8:05 PM, Justin Lemkul wrote: > > > On 9/30/14 10:30 AM, Anurag Dobhal wrote: > >> Dear justin >> >> Thank you for your rely and precious time. >> >> I am aware that .gro file is to be visualized in VMD and its content can >> be >> checked in text editor. >> all the previous .gro file are visualized and checked in VMD. >> >> I have obetained that ( confout.gro )file by running the command of energy >> minimization i.e. >> >> "mdrun -v -deffnm em" >> >> and before this command I ran the command >> >> "perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat" >> >> >> after running the energy minimization the confout.gro is actually >> obetained as >> >> confout.gro.trr. so I am renaming it as confout.gro. so it is actually >> .trr format, which can not be visualised in VMD or checked in text >> editor. >> >> > Which means it's an invalid input file format and that's why you're > getting a failure from InflateGRO. If file names are given different > extensions, you can't just randomly change them and expect things to work. > If you ran > > mdrun -v -deffnm em > > you will never get anything named confout.gro. Note that the tutorial > explicitly says: > > Then, scale down the lipids by a factor of 0.95 (assuming you have used > default names, the result of the minimization is called "confout.gro" > > You didn't use default names. You told mdrun "name all of my files em.*" > when you invoked -deffnm. If you simply ran: > > mdrun -s em.tpr > > you would get confout.gro. In any case, you should have "em.gro" which is > what you should use to proceed. I have no idea where confout.gro.trr came > from, but it's a trajectory and clearly not what needs to be used here. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
Dear justin Thank you for your rely and precious time. I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous .gro file are visualized and checked in VMD. I have obetained that ( confout.gro )file by running the command of energy minimization i.e. "mdrun -v -deffnm em" and before this command I ran the command "perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat" after running the energy minimization the confout.gro is actually obetained as confout.gro.trr. so I am renaming it as confout.gro. so it is actually .trr format, which can not be visualised in VMD or checked in text editor. Please help. On Tue, Sep 30, 2014 at 4:41 PM, Justin Lemkul wrote: > > > On 9/30/14 7:06 AM, Anurag Dobhal wrote: > >> Thank you Justin for your reply >> >> as per your suggestion i verified the contents in confout.gro but i was >> unable to check file as when i am clicking on it to open it I am getting >> an >> message that file is of unknown type. >> >> > A .gro file is not simply something that you click on to magically open. > It's just a listing of coordinates. Visualize it in VMD. Inspect its > contents with a text editor. > > -Justin > > > I again repeated the tutorial and I am getting the same things. >> >> Thank you again for your time. >> >> On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul wrote: >> >> >>> >>> On 9/30/14 5:51 AM, Anurag Dobhal wrote: >>> >>> Hello gromacs users. >>>> >>>> >>>> I am running GROMACS Tutorial of KALP15 in DPPC. >>>> >>>> I am in the step define box and solvate. >>>> >>>> after the command >>>> >>>> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 >>>> area_shrink1.dat >>>> >>>> >>>> i am getting an error as >>>> >>>> Use of uninitialized value $box_x in multiplication (*) at >>>> inflategro.pl line 339. >>>> Use of uninitialized value $box_y in multiplication (*) at >>>> inflategro.pl line 340. >>>> Scaling lipids >>>> There are 0 lipids... >>>> Illegal division by zero at inflategro.pl line 380. >>>> >>>> I am repeating the step third time and I am getting the same error. >>>> >>>> please help me how to skip this error. >>>> >>>> >>>> I suggested you verify the contents of confout.gro are sensible. What >>> did >>> you learn? >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> 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. >>> >>> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
Thank you Justin for your reply as per your suggestion i verified the contents in confout.gro but i was unable to check file as when i am clicking on it to open it I am getting an message that file is of unknown type. I again repeated the tutorial and I am getting the same things. Thank you again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul wrote: > > > On 9/30/14 5:51 AM, Anurag Dobhal wrote: > >> Hello gromacs users. >> >> >> I am running GROMACS Tutorial of KALP15 in DPPC. >> >> I am in the step define box and solvate. >> >> after the command >> >> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 >> area_shrink1.dat >> >> >> i am getting an error as >> >> Use of uninitialized value $box_x in multiplication (*) at >> inflategro.pl line 339. >> Use of uninitialized value $box_y in multiplication (*) at >> inflategro.pl line 340. >> Scaling lipids >> There are 0 lipids... >> Illegal division by zero at inflategro.pl line 380. >> >> I am repeating the step third time and I am getting the same error. >> >> please help me how to skip this error. >> >> > I suggested you verify the contents of confout.gro are sensible. What did > you learn? > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. Thank you. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding GROMACS Tutorial "KALP15 in DPPC"
hello justin Can you please tell me how will i solvate my system. which command will i use and what will be my input and output file. Thanks for your help Anurag dobhal On Sun, Sep 28, 2014 at 6:58 PM, Justin Lemkul wrote: > > > On 9/28/14 9:14 AM, Anurag Dobhal wrote: > >> Hey gromacs users >> >> I got the confout.gro file by running the command >> >> mdrun -v -deffnm em -o confout.gro >> >> and then i ran the command " perl inflategro.pl confout.gro 0.95 DPPC >> 0 system_shrink1.gro 5 area_shrink1.dat " >> >> but now the teminal says that >> >> Reading. >> Use of uninitialized value $box_x in multiplication (*) at >> inflategro.pl line 339. >> Use of uninitialized value $box_y in multiplication (*) at >> inflategro.pl line 340. >> Scaling lipids >> There are 0 lipids... >> Illegal division by zero at inflategro.pl line 380 >> >> >> is this output is expected ??? >> >> > No, fatal errors like that are not expected. If EM successfully completed > and wrote a confout.gro file, there should be no problem. Visualize > confout.gro and make sure its contents are sane. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding GROMACS Tutorial "KALP15 in DPPC"
Hey gromacs users I got the confout.gro file by running the command mdrun -v -deffnm em -o confout.gro and then i ran the command " perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat " but now the teminal says that Reading. Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380 is this output is expected ??? please guide me. Thank you On Sun, Sep 28, 2014 at 6:33 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear users. > > > I am doing the tutorial "KALP15 in DPPC". > > I heve done till the command > > perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat > > and then i minimised the the system by running the command > > mdrun -v -deffnm em > > now i am unable to understand how to produce "confout.gro" > > > please help how to proceed and where I am wrong. > > > Thank you > > > Anurag Dobhal > > > On Sun, Sep 28, 2014 at 5:37 PM, Anurag Dobhal < > anurag.dob...@nano-medicine.co.in> wrote: > >> Dear users. >> >> >> I am doing the tutorial "KALP15 in DPPC". >> >> I heve done till the command >> >> "genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 >> 10" >> >> after that I am not able to understand wat to do and how to solvate the >> system. >> >> please can anyone expalin me in easy words how to proceed. >> >> Please help >> >> >> Anurag Dobhal >> >> >> >> >> >> > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding GROMACS Tutorial "KALP15 in DPPC"
Dear users. I am doing the tutorial "KALP15 in DPPC". I heve done till the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat and then i minimised the the system by running the command mdrun -v -deffnm em now i am unable to understand how to produce "confout.gro" please help how to proceed and where I am wrong. Thank you Anurag Dobhal On Sun, Sep 28, 2014 at 5:37 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear users. > > > I am doing the tutorial "KALP15 in DPPC". > > I heve done till the command > > "genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 > 10" > > after that I am not able to understand wat to do and how to solvate the > system. > > please can anyone expalin me in easy words how to proceed. > > Please help > > > Anurag Dobhal > > > > > > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding GROMACS Tutorial "KALP15 in DPPC"
Dear users. I am doing the tutorial "KALP15 in DPPC". I heve done till the command "genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10" after that I am not able to understand wat to do and how to solvate the system. please can anyone expalin me in easy words how to proceed. Please help Anurag Dobhal -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding siRNA simulation.
I am simulating an RNA molecule in which first residue has a 5'-PO4 cap, which is uncommon. I am adding the atoms and bond parameters in the .rtp files in the existing force field directories but these parameters are not getting saved. I am using Amber 99 force field and i am making changes in the rna.rtp file. How can i make these changes possible. Do I need to write new .rtp file. please help -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding error in grompp while running the tutorial of " KALP15 in DPPC "
I am getting an error while running the commmand gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr Fatal error: Unknown atomtype OW please help !!! -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding gromacs installation
I have followed the following steps for installaing gromacs 5.0.1 tar xfz gromacs-5.0.1.tar.gz cd gromacs-5.0.1 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC please tell me weather these steps are enough to install gromacs or do i need to do some thing more. please help. Anurag Dobhal -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding error in grompp while running the tutorial of " KALP15 in DPPC "
I am getting an error while running the commmand gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr Fatal error: Unknown bond_atomtype MNH3 please help -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding error in grompp while running the tutorial of " KALP15 in DPPC "
I am getting an error while running the commmand gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr Fatal error: Unknown bond_atomtype MNH3 -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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.
