[gmx-users] Trouble with the command "g_x2top"
Dear all, I had trouble with the command "g_x2top" while trying to generate the topology file for the molecule SAM. Error came up as followed. Program g_x2top, VERSION 4.5.5 Source code file: g_x2top.c, line: 505 Fatal error: No or incorrect atomname2type.n2t file found (looking for amber94.ff) Does anyone know what could have caused this problem? Thanks in advance Felix Weng -- View this message in context: http://gromacs.5086.x6.nabble.com/Trouble-with-the-command-g-x2top-tp5013277.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Trouble with the command "g_x2top"
Dear all, I had trouble with the command "g_x2top" while trying to generate the topology file for the molecule SAM. Error came up as followed. Program g_x2top, VERSION 4.5.5 Source code file: g_x2top.c, line: 505 Fatal error: No or incorrect atomname2type.n2t file found (looking for amber94.ff) Does anyone know what could have caused this problem? Thanks in advance Felix Weng -- 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] Installing Gromacs 4.6.3 using Cygwin
On 11.12.2013 17:48, chem grad wrote: I am new to both Cygwin and Gromacs, so I apologize in advance if this error is do to my computing ignorance. I downloaded the gromacs-4.6.3.tar.gz file and tried to follow the 'Quick and Dirty Installation Instructions' to install Gromacs 4.6.3 on my new Windows 8 machine, but encountered a couple snags. ... src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_single.c.o make[2]: *** No rule to make target '//cygdrive/c/Cygwin/home/kelly/Gromacs/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', needed by 'src/gmxlib/cyggmx-8.dll'. Stop. Simple answer: use the fftw3-3.3.3 that comes with your cygwin/64-distribution. Gromacs will find and use it. The performance of this fftw3 (it lacks SSE2) should be close to the one you'd compile for yourself on the machine (I tested both). Otherwise: download and compile fftw3 in cygwin and use this local build for Gromacs. GMX_BUILD_OWN_FFTW doesn't seem to work for now in cygwin. If you are interested, I could provide detailed instructions for both fftw3 and Gromacs on cygwin/64. Regards M. -- 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] Normal Mode Analysis with Gromacs 4.6
Why are you using PME-switch? Without explicitly choosing a switch? Mark On Thu, Dec 12, 2013 at 6:45 PM, mcfc1301 wrote: > Hello Everyone， > > I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot > but > find little useful. > My Gromacs was installed in a Linux cluster. > > Follows is my steps to do normal mode analysis: > > • pdb2gmx -ignh -ff < forcefield > -f -o mut.gro -p topol.top > • editconf -f mut.gro -o box.gro -d 1.5 > • grompp -f em.mdp -c box.gro -p topol.top -o em.tpr > • mdrun -s em.tpr -deffnm em -c em.g96 -v > • grompp -f nm.mdp -c em.g96 -o nm.tpr > --->WARNING 1 [file nm.mdp]: > The switching range for PME-Switch should be 5% or > less, energy > conservation will be good anyhow, since ewald_rtol > = > 1e-05 > > I have taken advises from the forum that I should not genbox and should use > cg instead steep for em in order to do Normal Mode Analysis, but now I am > facing problem of PME-Switch. > > Does anyone have any experience on this? > > Thanks in advance. > > Kevin > > > ==Attached is em.mdp and nm.mdp= > em.mdp > > define = -DFLEXIBLE > constraints = none > integrator = cg > dt = 0.002; ps ! > nsteps = 400 > nstlist = 10 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb= 1.0 > vdwtype = cut-off > rvdw= 1.4 > optimize_fft= yes > emtol = 1000 > emstep = 0.01 > > --- > nm.mdp > constraints = none > integrator = nm > dt = 0.002; ps ! > nsteps = 400 > nstlist = 10 > ns_type = grid > rlist = 1.2 > coulombtype = PME-Switch > rcoulomb= 1.0 > vdwtype = Cut-off > rvdw= 1.4 > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Normal-Mode-Analysis-with-Gromacs-4-6-tp5013240p5013276.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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.
Re: [gmx-users] pressure based replica exchange
Quite right, sorry. P as the control variable is not implemented. NPT with T as the control variable is, for example. Mark On Thu, Dec 12, 2013 at 5:58 PM, Michael Shirts wrote: > Pressure replica exchange is not in currently. It will be added > eventually (it's not that hard, just takes time, and hasn't been a > priority.). > > Note that pressure temperature control with berendsen pressure control > will be 100% wrong. For pressure replica exchange to work, the > barostat has to give the correct volume fluctuations, and berendsen > does not give correct volume fluctuations. > > Of course, that's irrelevant since pressure replica exchange isn't in yet. > > The exchange criteria is always of the form min(1,exp(-X), where X = > \beta(Delta (beta U) + Delta (beta P V)). Where P, beta, and U can > vary with state. > > What is in is temperature replica exchange with NPT, where beta > changes, but P stays the same. > > On Thu, Dec 12, 2013 at 1:40 AM, Jianguo Li wrote: > > Thanks very much. As you suggested, making T with small increments such > as 300.0, 300.0001, 300.0002 ... leads to complaints :-) > > > > I am trying to do replica exchange at different surface tensions for my > membrane system. > > To achieve different surface tensions for different replica, I only > changed Pxy, but keep Pz the same for all replica. > > pcoupl = berendsen > > pcoupltype = semi-isotropic > > tau_p = 0.5 0.5 > > ref_p = 1.0 1.0 ; Pxy and Pz > > compressibility = 4.5e-5 4.5e-5 > > > > I noticed that in the manual, the eq (3.141) shows the exchange > probability. Can you explain what does the P1 and P2 represent? Pxy or Pz? > > > > Also, the manual mentioned about using Hamiltonian and temperature > replica exchange simultaneously (eq 3.143). But there is no pressure term > in the acceptance criteria (eq 3.143). I am wondering if > pressure+temperature+Hamiltonian replica exchange has been implemented in > Gromacs. If yes, what is the general equation of acceptance criteria? > > > > Cheers, > > Jianguo > > > > > > > > > > > > > > > > On Tuesday, 10 December 2013, 17:49, Mark Abraham < > mark.j.abra...@gmail.com> wrote: > > > > > > > > > > > > > > On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li wrote: > > > > Dear All, > >> > >>Is it possible to do pressure based replica exchange simulations in > gromacs? Basically I want to do replica exchange simulations for my > membrane system at different surface tensions. If I just set different > pressures in the mpd file, then the mdrun will complain "systems are all > the same, there is nothing to exchange". Is there any other parameters I > need to set? > >> > > > > Yes, the implementation is a bit broken, and requires that one of ref-t > or lambda varies before it even considers the pressure. If you want T > constant and P as the replica control variable, you can can only do that by > fooling the implementation by having T vary in tiny increments. > > > > Mark > > > > > >>Thanks a lot! > >> > >>Jianguo > >>-- > >>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.
Re: [gmx-users] pressure based replica exchange
I'm not sure if pressure-based REMD is possible, but PLUMED-2.0 provides a quite flexible implementation of Hamiltonian REMD for GROMACS. It may be worth-checking it: http://arxiv.org/abs/1307.5144 On 12 December 2013 12:11, Mark Abraham wrote: > Quite right, sorry. P as the control variable is not implemented. NPT with > T as the control variable is, for example. > > Mark > > > On Thu, Dec 12, 2013 at 5:58 PM, Michael Shirts > wrote: > > > Pressure replica exchange is not in currently. It will be added > > eventually (it's not that hard, just takes time, and hasn't been a > > priority.). > > > > Note that pressure temperature control with berendsen pressure control > > will be 100% wrong. For pressure replica exchange to work, the > > barostat has to give the correct volume fluctuations, and berendsen > > does not give correct volume fluctuations. > > > > Of course, that's irrelevant since pressure replica exchange isn't in > yet. > > > > The exchange criteria is always of the form min(1,exp(-X), where X = > > \beta(Delta (beta U) + Delta (beta P V)). Where P, beta, and U can > > vary with state. > > > > What is in is temperature replica exchange with NPT, where beta > > changes, but P stays the same. > > > > On Thu, Dec 12, 2013 at 1:40 AM, Jianguo Li wrote: > > > Thanks very much. As you suggested, making T with small increments such > > as 300.0, 300.0001, 300.0002 ... leads to complaints :-) > > > > > > I am trying to do replica exchange at different surface tensions for my > > membrane system. > > > To achieve different surface tensions for different replica, I only > > changed Pxy, but keep Pz the same for all replica. > > > pcoupl = berendsen > > > pcoupltype = semi-isotropic > > > tau_p = 0.5 0.5 > > > ref_p = 1.0 1.0 ; Pxy and Pz > > > compressibility = 4.5e-5 4.5e-5 > > > > > > I noticed that in the manual, the eq (3.141) shows the exchange > > probability. Can you explain what does the P1 and P2 represent? Pxy or > Pz? > > > > > > Also, the manual mentioned about using Hamiltonian and temperature > > replica exchange simultaneously (eq 3.143). But there is no pressure term > > in the acceptance criteria (eq 3.143). I am wondering if > > pressure+temperature+Hamiltonian replica exchange has been implemented in > > Gromacs. If yes, what is the general equation of acceptance criteria? > > > > > > Cheers, > > > Jianguo > > > > > > > > > > > > > > > > > > > > > > > > On Tuesday, 10 December 2013, 17:49, Mark Abraham < > > mark.j.abra...@gmail.com> wrote: > > > > > > > > > > > > > > > > > > > > > On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li > wrote: > > > > > > Dear All, > > >> > > >>Is it possible to do pressure based replica exchange simulations in > > gromacs? Basically I want to do replica exchange simulations for my > > membrane system at different surface tensions. If I just set different > > pressures in the mpd file, then the mdrun will complain "systems are all > > the same, there is nothing to exchange". Is there any other parameters I > > need to set? > > >> > > > > > > Yes, the implementation is a bit broken, and requires that one of ref-t > > or lambda varies before it even considers the pressure. If you want T > > constant and P as the replica control variable, you can can only do that > by > > fooling the implementation by having T vary in tiny increments. > > > > > > Mark > > > > > > > > >>Thanks a lot! > > >> > > >>Jianguo > > >>-- > > >>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/
[gmx-users] Creating a topology file for small molecules
Dear all, I've been having trouble creating a topology file for small molecules SAM and PA. I've tried using ATB, PRODRG, as wel as the command g_x2top, but with no success. Does anyone know any other ways to create a topology file for small molecues for GROMACS? Thanks in advance. Felix Weng -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-topology-file-for-small-molecules-tp5013281.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Creating a topology file for small molecules
google acpype. On 12 December 2013 10:57, Felix Weng <100711...@gms.tcu.edu.tw> wrote: > Dear all, > > I've been having trouble creating a topology file for small molecules SAM > and PA. I've tried using ATB, PRODRG, as wel as the command g_x2top, but > with no success. > > Does anyone know any other ways to create a topology file for small > molecues > for GROMACS? > > Thanks in advance. > > Felix Weng > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Creating-a-topology-file-for-small-molecules-tp5013281.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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] g_tcaf issue
Hi all. I'm sorry if this message goes repeated. But here it seems that it never arrived at the mail-list. We are having some problem running g_tcaf here. It keeps yielding "segmentation faults". We first thought it was because of the single-precision calculations of the first run, or the exceedingly large trajectory file. Both were changed for a second trial, which still yielded the same error. Also, we are aware of the similar error posted in this thread at this mail-list: http://www.mail-archive.com/gmx-users@gromacs.org/msg54295.html Unfortunately, it seems to be a different issue. We are also writing a full trajectory file in the .trr file, as can be seen below on the excerpt from the .mdp file below: dt = 0.002 nsteps = 10 nstcomm = 1 nstxout = 0 nstvout = 10 nstfout = 10 nstlog = 10 nstenergy = 100 nstlist = 5 The precise line our cluster script is trying to execute is: echo 0 | g_tcaf -f BMIm.AlCl4.md14.trr -s BMIm.AlCl4.md14.tpr -oa BMIm.AlCl4.md14.all.xvg -o BMIm.AlCl4.md14.tcaf.xvg -of BMIm.AlCl4.md14.fit.xvg -ov BMIm.AlCl4.md14.visc.xvg >& md14.tcaf.out The "echo 0" assures that the needed parameter is passed to g_tcaf. By the way, in our last test the pbs parameters for resources request were: #PBS -l ncpus=8 #PBS -l mem=16GB We know that it's pointless to ask for extra cpus, it's in there just for a matter involving the machine architecture. But the 16 GB of memory, despite available, are just our guess on how much it will need. We also tested it out of the queue to be certain, but it still fails at the same point. Does anybody has any suggestion please? I would be really helpful. Thanks a lot in advance for any help, Jones -- 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] Distance restraints does not work?
Hi, I am trying to do a simulation with distance restraints for the Zn-His(NE2)atoms in a peptide, but the distances are not kept to what I want them to be. Why? I have added this in my topology.top: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif #ifdef ZN [ distance_restraints ] 355333 1 1 1 0.1985 0.2231 0.4 1 355316 1 2 1 0.1985 0.2231 0.4 1 355156 1 3 1 0.1985 0.2231 0.4 1 355139 1 4 1 0.1985 0.2231 0.4 1 #endif And I use the following setting in pr.mdp: define = -DZN ; NMR refinement stuff disre = Simple; Distance restraints type: No, Simple or Ensemble disre-weighting = Equal ; Force weighting of pairs in one dist rest: Equal or Conservative disre-mixed = no; Use sqrt of the time averaged times the instantaneous violation disre-fc= 1000 disre-tau = 0 nstdisreout = 100 ; Output frequency for pair distances to energy file When I look at the structure, two of the restrained His(atom 139 and 333) has left the Zn(atom 355). Some values from the distance analysis are printed below: g_dist -f traj.trr -s b4pr.tpr -n index.ndx -o dist139.xvg less dist139.xvg @xaxis label "Time (ps)" @yaxis label "Distance (nm)" @ s0 legend "|d|" 0.0000.2119962 24.0000.2470244 50.0000.4642269 100.0000.4505744 less dist333.xvg @xaxis label "Time (ps)" @yaxis label "Distance (nm)" @ s0 legend "|d|" 0.0000.2172887 24.0000.2171661 50.0000.4632832 100.0000.301 Why does the distance increase? Why is it not held in between roughly 0.1985 0.2231? Thanks in advance, -- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö +46 480 446 152 Telephone +46 73 905 7186 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg -- 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] Trouble with the command "g_x2top"
On Thu, Dec 12, 2013 at 3:43 AM, Felix Weng <100711...@gms.tcu.edu.tw>wrote: > Dear all, > > I had trouble with the command "g_x2top" while trying to generate the > topology file for the molecule SAM. Error came up as followed. > > Program g_x2top, VERSION 4.5.5 > Source code file: g_x2top.c, line: 505 > > Fatal error: > No or incorrect atomname2type.n2t file found (looking for amber94.ff) > > Does anyone know what could have caused this problem? > > Exactly what the fatal error says - that force field does not have an .n2t file. As I recall, only OPLS and maybe one of the Gromos parameter sets has an .n2t file. You will have to create one yourself, but in this case that probably winds up being more work than deriving the parameters through some other means. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] Distance restraints does not work?
On Thu, Dec 12, 2013 at 8:22 AM, Emma Ahlstrand wrote: > Hi, > I am trying to do a simulation with distance restraints for the > Zn-His(NE2)atoms in a peptide, but the distances are not kept to what I > want them to be. Why? > > I have added this in my topology.top: > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > #ifdef ZN > [ distance_restraints ] > 355333 1 1 1 0.1985 0.2231 0.4 1 > 355316 1 2 1 0.1985 0.2231 0.4 1 > 355156 1 3 1 0.1985 0.2231 0.4 1 > 355139 1 4 1 0.1985 0.2231 0.4 1 > #endif > > And I use the following setting in pr.mdp: > define = -DZN > ; NMR refinement stuff > disre = Simple; Distance restraints type: No, Simple or > Ensemble > disre-weighting = Equal ; Force weighting of pairs in one dist > rest: Equal or Conservative > disre-mixed = no; Use sqrt of the time averaged times the > instantaneous violation > disre-fc= 1000 > disre-tau = 0 > nstdisreout = 100 ; Output frequency for pair distances to > energy file > > When I look at the structure, two of the restrained His(atom 139 and 333) > has left the Zn(atom 355). Some values from the distance analysis are > printed below: > g_dist -f traj.trr -s b4pr.tpr -n index.ndx -o dist139.xvg > less dist139.xvg > @xaxis label "Time (ps)" > @yaxis label "Distance (nm)" > @ s0 legend "|d|" >0.0000.2119962 > 24.0000.2470244 > 50.0000.4642269 > 100.0000.4505744 > > less dist333.xvg > @xaxis label "Time (ps)" > @yaxis label "Distance (nm)" > @ s0 legend "|d|" > 0.0000.2172887 > 24.0000.2171661 > 50.0000.4632832 > 100.0000.301 > > Why does the distance increase? Why is it not held in between roughly > 0.1985 0.2231? > > A restraint is a penalty. It does not absolutely fix certain quantities, so the distances can deviate. This is especially true when you have multiple restraints that must be simultaneously satisfied - they compete with one another. Note the functional forms in the manual; your settings indicate that no penalty is applied between 0.1985 and 0.2231 nm, and only after 0.4 nm is a large penalty imposed. So there's a fair amount of wiggle room there for each restraint. You can adjust the coefficients to produce a better result, or simply introduce constraints for these "bonds," in which case the originally geometry will be preserved exactly. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] Distance restraints does not work?
use mdp option disre=simple Your output should contain a NOTE telling you this: http://redmine.gromacs.org/issues/265 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Emma Ahlstrand Sent: 12 December 2013 08:22 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Distance restraints does not work? Hi, I am trying to do a simulation with distance restraints for the Zn-His(NE2)atoms in a peptide, but the distances are not kept to what I want them to be. Why? I have added this in my topology.top: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif #ifdef ZN [ distance_restraints ] 355333 1 1 1 0.1985 0.2231 0.4 1 355316 1 2 1 0.1985 0.2231 0.4 1 355156 1 3 1 0.1985 0.2231 0.4 1 355139 1 4 1 0.1985 0.2231 0.4 1 #endif And I use the following setting in pr.mdp: define = -DZN ; NMR refinement stuff disre = Simple; Distance restraints type: No, Simple or Ensemble disre-weighting = Equal ; Force weighting of pairs in one dist rest: Equal or Conservative disre-mixed = no; Use sqrt of the time averaged times the instantaneous violation disre-fc= 1000 disre-tau = 0 nstdisreout = 100 ; Output frequency for pair distances to energy file When I look at the structure, two of the restrained His(atom 139 and 333) has left the Zn(atom 355). Some values from the distance analysis are printed below: g_dist -f traj.trr -s b4pr.tpr -n index.ndx -o dist139.xvg less dist139.xvg @xaxis label "Time (ps)" @yaxis label "Distance (nm)" @ s0 legend "|d|" 0.0000.2119962 24.0000.2470244 50.0000.4642269 100.0000.4505744 less dist333.xvg @xaxis label "Time (ps)" @yaxis label "Distance (nm)" @ s0 legend "|d|" 0.0000.2172887 24.0000.2171661 50.0000.4632832 100.0000.301 Why does the distance increase? Why is it not held in between roughly 0.1985 0.2231? Thanks in advance, -- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö +46 480 446 152 Telephone +46 73 905 7186 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] modifying LJ interactions in Hamiltonian REMD
Dear all, I am trying to set up a Hamiltonian REMD simulation of a peptide interacting with ions in solution. In order to avoid salt bridges and thus to increase the conformational sampling, my idea was to weaken the LJ interactions between the oxygen atoms of the side chains and the cations in solution. However, after studying the manual and the mailing list, I still haven't been able to figure out the proper way to define the modified LJ parameters of the oxygen-cation interactions in state B. Is there a simple way of doing this or do I need to define a new atomtype? Thanks in advance, Jens -- 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] pressure based replica exchange
Thanks Michael and Mark. Implementation of the pressure based replica exchange will be useful for membrane systems as membranes will be unstable using temperature based replica exchange. Btw, I noticed there is a recent paper on surface tension replica exchange simulations of membranes: http://pubs.acs.org/doi/abs/10.1021/ct400445k I will wait for the future versions of gromacs, hope it will be implemented soon :-) Cheers Jianguo On Thursday, 12 December 2013, 14:58, Michael Shirts wrote: Pressure replica exchange is not in currently. It will be added eventually (it's not that hard, just takes time, and hasn't been a priority.). Note that pressure temperature control with berendsen pressure control will be 100% wrong. For pressure replica exchange to work, the barostat has to give the correct volume fluctuations, and berendsen does not give correct volume fluctuations. Of course, that's irrelevant since pressure replica exchange isn't in yet. The exchange criteria is always of the form min(1,exp(-X), where X = \beta(Delta (beta U) + Delta (beta P V)). Where P, beta, and U can vary with state. What is in is temperature replica exchange with NPT, where beta changes, but P stays the same. On Thu, Dec 12, 2013 at 1:40 AM, Jianguo Li wrote: > Thanks very much. As you suggested, making T with small increments such as > 300.0, 300.0001, 300.0002 ... leads to complaints :-) > > I am trying to do replica exchange at different surface tensions for my > membrane system. > To achieve different surface tensions for different replica, I only changed > Pxy, but keep Pz the same for all replica. > pcoupl = berendsen > pcoupltype = semi-isotropic > tau_p = 0.5 0.5 > ref_p = 1.0 1.0 ; Pxy and Pz > compressibility = 4.5e-5 4.5e-5 > > I noticed that in the manual, the eq (3.141) shows the exchange probability. > Can you explain what does the P1 and P2 represent? Pxy or Pz? > > Also, the manual mentioned about using Hamiltonian and temperature replica > exchange simultaneously (eq 3.143). But there is no pressure term in the > acceptance criteria (eq 3.143). I am wondering if > pressure+temperature+Hamiltonian replica exchange has been implemented in > Gromacs. If yes, what is the general equation of acceptance criteria? > > Cheers, > Jianguo > > > > > > > > On Tuesday, 10 December 2013, 17:49, Mark Abraham > wrote: > > > > > > > On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li wrote: > > Dear All, >> >>Is it possible to do pressure based replica exchange simulations in gromacs? >>Basically I want to do replica exchange simulations for my membrane system at >>different surface tensions. If I just set different pressures in the mpd file, then the mdrun will complain "systems are all the same, there is nothing to exchange". Is there any other parameters I need to set? >> > > Yes, the implementation is a bit broken, and requires that one of ref-t or > lambda varies before it even considers the pressure. If you want T constant > and P as the replica control variable, you can can only do that by fooling > the implementation by having T vary in tiny increments. > > Mark > > >>Thanks a lot! >> >>Jianguo >>-- >>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.
Re: [gmx-users] pressure based replica exchange
Thanks for the paper, I will look at it! Cheers Jianguo On Thursday, 12 December 2013, 18:54, Thomas Evangelidis wrote: I'm not sure if pressure-based REMD is possible, but PLUMED-2.0 provides a quite flexible implementation of Hamiltonian REMD for GROMACS. It may be worth-checking it: http://arxiv.org/abs/1307.5144 On 12 December 2013 12:11, Mark Abraham wrote: > Quite right, sorry. P as the control variable is not implemented. NPT with > T as the control variable is, for example. > > Mark > > > On Thu, Dec 12, 2013 at 5:58 PM, Michael Shirts > wrote: > > > Pressure replica exchange is not in currently. It will be added > > eventually (it's not that hard, just takes time, and hasn't been a > > priority.). > > > > Note that pressure temperature control with berendsen pressure control > > will be 100% wrong. For pressure replica exchange to work, the > > barostat has to give the correct volume fluctuations, and berendsen > > does not give correct volume fluctuations. > > > > Of course, that's irrelevant since pressure replica exchange isn't in > yet. > > > > The exchange criteria is always of the form min(1,exp(-X), where X = > > \beta(Delta (beta U) + Delta (beta P V)). Where P, beta, and U can > > vary with state. > > > > What is in is temperature replica exchange with NPT, where beta > > changes, but P stays the same. > > > > On Thu, Dec 12, 2013 at 1:40 AM, Jianguo Li wrote: > > > Thanks very much. As you suggested, making T with small increments such > > as 300.0, 300.0001, 300.0002 ... leads to complaints :-) > > > > > > I am trying to do replica exchange at different surface tensions for my > > membrane system. > > > To achieve different surface tensions for different replica, I only > > changed Pxy, but keep Pz the same for all replica. > > > pcoupl = berendsen > > > pcoupltype = semi-isotropic > > > tau_p = 0.5 0.5 > > > ref_p = 1.0 1.0 ; Pxy and Pz > > > compressibility = 4.5e-5 4.5e-5 > > > > > > I noticed that in the manual, the eq (3.141) shows the exchange > > probability. Can you explain what does the P1 and P2 represent? Pxy or > Pz? > > > > > > Also, the manual mentioned about using Hamiltonian and temperature > > replica exchange simultaneously (eq 3.143). But there is no pressure term > > in the acceptance criteria (eq 3.143). I am wondering if > > pressure+temperature+Hamiltonian replica exchange has been implemented in > > Gromacs. If yes, what is the general equation of acceptance criteria? > > > > > > Cheers, > > > Jianguo > > > > > > > > > > > > > > > > > > > > > > > > On Tuesday, 10 December 2013, 17:49, Mark Abraham < > > mark.j.abra...@gmail.com> wrote: > > > > > > > > > > > > > > > > > > > > > On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li > wrote: > > > > > > Dear All, > > >> > > >>Is it possible to do pressure based replica exchange simulations in > > gromacs? Basically I want to do replica exchange simulations for my > > membrane system at different surface tensions. If I just set different > > pressures in the mpd file, then the mdrun will complain "systems are all > > the same, there is nothing to exchange". Is there any other parameters I > > need to set? > > >> > > > > > > Yes, the implementation is a bit broken, and requires that one of ref-t > > or lambda varies before it even considers the pressure. If you want T > > constant and P as the replica control variable, you can can only do that > by > > fooling the implementation by having T vary in tiny increments. > > > > > > Mark > > > > > > > > >>Thanks a lot! > > >> > > >>Jianguo > > >>-- > > >>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
Re: [gmx-users] pressure based replica exchange
Hamiltonian replica exchange based around the free energy functionality is in GROMACS, though it would be interesting to explore the PLUMED options more to understand the differences . . . On Thu, Dec 12, 2013 at 5:48 AM, Thomas Evangelidis wrote: > I'm not sure if pressure-based REMD is possible, but PLUMED-2.0 provides a > quite flexible implementation of Hamiltonian REMD for GROMACS. It may be > worth-checking it: > > http://arxiv.org/abs/1307.5144 > > > > > On 12 December 2013 12:11, Mark Abraham wrote: > >> Quite right, sorry. P as the control variable is not implemented. NPT with >> T as the control variable is, for example. >> >> Mark >> >> >> On Thu, Dec 12, 2013 at 5:58 PM, Michael Shirts >> wrote: >> >> > Pressure replica exchange is not in currently. It will be added >> > eventually (it's not that hard, just takes time, and hasn't been a >> > priority.). >> > >> > Note that pressure temperature control with berendsen pressure control >> > will be 100% wrong. For pressure replica exchange to work, the >> > barostat has to give the correct volume fluctuations, and berendsen >> > does not give correct volume fluctuations. >> > >> > Of course, that's irrelevant since pressure replica exchange isn't in >> yet. >> > >> > The exchange criteria is always of the form min(1,exp(-X), where X = >> > \beta(Delta (beta U) + Delta (beta P V)). Where P, beta, and U can >> > vary with state. >> > >> > What is in is temperature replica exchange with NPT, where beta >> > changes, but P stays the same. >> > >> > On Thu, Dec 12, 2013 at 1:40 AM, Jianguo Li wrote: >> > > Thanks very much. As you suggested, making T with small increments such >> > as 300.0, 300.0001, 300.0002 ... leads to complaints :-) >> > > >> > > I am trying to do replica exchange at different surface tensions for my >> > membrane system. >> > > To achieve different surface tensions for different replica, I only >> > changed Pxy, but keep Pz the same for all replica. >> > > pcoupl = berendsen >> > > pcoupltype = semi-isotropic >> > > tau_p = 0.5 0.5 >> > > ref_p = 1.0 1.0 ; Pxy and Pz >> > > compressibility = 4.5e-5 4.5e-5 >> > > >> > > I noticed that in the manual, the eq (3.141) shows the exchange >> > probability. Can you explain what does the P1 and P2 represent? Pxy or >> Pz? >> > > >> > > Also, the manual mentioned about using Hamiltonian and temperature >> > replica exchange simultaneously (eq 3.143). But there is no pressure term >> > in the acceptance criteria (eq 3.143). I am wondering if >> > pressure+temperature+Hamiltonian replica exchange has been implemented in >> > Gromacs. If yes, what is the general equation of acceptance criteria? >> > > >> > > Cheers, >> > > Jianguo >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > On Tuesday, 10 December 2013, 17:49, Mark Abraham < >> > mark.j.abra...@gmail.com> wrote: >> > > >> > > >> > > >> > > >> > > >> > > >> > > On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li >> wrote: >> > > >> > > Dear All, >> > >> >> > >>Is it possible to do pressure based replica exchange simulations in >> > gromacs? Basically I want to do replica exchange simulations for my >> > membrane system at different surface tensions. If I just set different >> > pressures in the mpd file, then the mdrun will complain "systems are all >> > the same, there is nothing to exchange". Is there any other parameters I >> > need to set? >> > >> >> > > >> > > Yes, the implementation is a bit broken, and requires that one of ref-t >> > or lambda varies before it even considers the pressure. If you want T >> > constant and P as the replica control variable, you can can only do that >> by >> > fooling the implementation by having T vary in tiny increments. >> > > >> > > Mark >> > > >> > > >> > >>Thanks a lot! >> > >> >> > >>Jianguo >> > >>-- >> > >>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.k
[gmx-users] Pressure coupling constants
Hi all I am using NPT ensemble to relax a highly compressed system. I find that the way it relaxes depends on the pressure coupling constant ( berendsen barostat). My question is if the choice of the coupling constant would depend on the system conditions? The compressed system would tend to at expand faster rate and accordingly one should use a coupling constant much smaller than usual? Thanks Santo - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA -- View this message in context: http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Pressure coupling constants
If the goal is to get the system to relax from a compressed state as part of preparation, then berendsen pressure coupling is the best way. However, it is not a physical method -- it overly constraints the volume distribution (which is one of the reasons it's good to force a system into a reasonable state). shorter tau_p and also short tau_t will help the relaxation occur without the simulation blowing up. If you want to get any meaningful physics at equilibration, then use MTTK or Parrinello-Rahman. None of the barostats are physically meaningful for nonequilibrium expansion or compression. On Thu, Dec 12, 2013 at 12:11 PM, kpsanto wrote: > Hi all > I am using NPT ensemble to relax a highly compressed system. I find that > the way it relaxes depends on the pressure coupling constant ( berendsen > barostat). My question is if the choice of the coupling constant would > depend on the system conditions? The compressed system would tend to at > expand faster rate and accordingly one should use a coupling constant much > smaller than usual? > > Thanks > Santo > > - > K. P. Santo > Post doctoral fellow > Department of Chemistry > University of North Carolina at Chapel Hill > Chapel Hill, NC, USA > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] OPLS force field parameters
Hi gmx users, I try to use OPLS force field for my simulation. I added the following residue to the aminoacids.rtp, but when I generate the topol.top file it does not show the the bond stretching, angle bond, dihedrals. [ NAF ] [ atoms ] C1opls_966 0.3846 1 C2opls_966 0.3846 1 C3opls_966 0.3846 1 C4opls_966 0.3846 1 F17 opls_972 -0.1923 1 F18 opls_972 -0.1923 1 F19 opls_972 -0.1923 1 F20 opls_972 -0.1923 1 F21 opls_972 -0.1923 1 F22 opls_972 -0.1923 1 F23 opls_972 -0.1923 1 F24 opls_972 -0.1923 1 C5opls_966 0.3846 1 C6opls_966 0.3846 1 C7opls_966 0.3846 1 C8opls_966 0.3846 1 F25 opls_972 -0.1923 1 F26 opls_972 -0.1923 1 F27 opls_972 -0.1923 1 F28 opls_972 -0.1923 1 F29 opls_972 -0.1923 1 F30 opls_972 -0.1923 1 F31 opls_972 -0.1923 1 F32 opls_972 -0.1923 1 C9opls_966 0.3846 1 C10 opls_966 0.3846 1 C11 opls_966 0.3846 1 C12 opls_966 0.3846 1 F33 opls_972 -0.1923 1 F34 opls_972 -0.1923 1 F35 opls_972 -0.1923 1 F36 opls_972 -0.1923 1 F37 opls_972 -0.1923 1 F38 opls_972 -0.1923 1 F39 opls_972 -0.1923 1 F40 opls_972 -0.1923 1 C13 opls_966 0.3846 1 C14 opls_966 0.3846 1 C15 opls_967 0.3218 1 C16 opls_966 0.3846 1 F41 opls_972 -0.1923 1 F42 opls_972 -0.1923 1 F43 opls_972 -0.1923 1 F44 opls_972 -0.1923 1 F45 opls_973 -0.1641 1 F46 opls_972 -0.1923 1 F47 opls_972 -0.1923 1 C48 opls_968 0.3228 1 O49 opls_980 -0.2742 1 C50 opls_969 0.401 1 O51 opls_981 -0.2604 1 C52 opls_967 0.3218 1 C53 opls_971 0.3216 1 F55 opls_974 -0.1637 1 F56 opls_974 -0.1637 1 F57 opls_975 -0.1932 1 C58 opls_970 0.4947 1 F59 opls_977 -0.1662 1 F60 opls_977 -0.1662 1 F61 opls_978 -0.3278 1 F62 opls_978 -0.3278 1 F66 opls_976 -0.1649 1 F67 opls_976 -0.1649 1 F68 opls_976 -0.1649 1 S54 opls_979 1.4124 1 O63 opls_982 -0.632 1 O64 opls_982 -0.632 1 O65 opls_982 -0.632 1 [ bonds ] C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C7 C7 C8 C8 C9 C9 C10 C10C11 C11C12 C12C13 C13C14 C14C15 C15C16 F17C1 F18C1 F19C2 F20C2 F21C3 F22C3 F23C4 F24C4 F25C5 F26C5 F27C6 F28C6 F29C7 F30C7 F31C8 F32C8 F33C9 F34C9 F35C10 F36C10 F37C11 F38C11 F39C12 F40C12 F41C13 F42C13 F43C14 F44C14 F45C15 F46C16 F47C16 C15O49 O49C48 F55C48 F56C48 C48C50 F57C50 C50C58 C58F66 C58F67 C58F68 C50O51 O51C52 C52F59 C52F60 C52C53 C53F61 C53F62 C53S54 S54O63 S54O64 S54O65 I added the bond description in the ffbonded.itp but it does not show in the topol.top file. In ffbonded.itp we have: [ bondtypes ] ; ij func b0 kb OWHW 10.09572 502080.0 ; For TIP4F Water - wlj 1/98 OWLP 10.01750 753120.0 ; -idem- C*HC 10.10800 284512.0 ; C1C2 10.16020 292880.0 ; C2C3 10.16020 292880.0 ; " I am not sure to put C C or C1 C2 here; I tried both, neither worked." [ angletypes ] ; ijk func th0 cth HW OW HW 1 109.500627.600 ; For TIP4F Water - wj 1/98 HW OW LP 154.750418.400 ; For TIP4F Water - wj 1/98 OU U OU 1 180.000 1255.200 ; J Phys Chem 97, 5685 (1993) HC C* CW 1 126.800292.880 ; HC C* CB 1 126.800292.880 ; HC CS CW 1 126.800292.880 ; However, the parameters that we had in topol file are different: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 5 1 [ angles ] ; aiajak funct
Re: [gmx-users] editconf and "conect" option
Thanks for your response. When I used the tpr file it DID work. When I tried the pdb file here is the error message I got: Program editconf, VERSION 4.5.4 Source code file: tpxio.c, line: 1970 Fatal error: Can not read file 50ps.pdb, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thanks, Steve -- View this message in context: http://gromacs.5086.x6.nabble.com/editconf-and-conect-option-tp5013271p5013295.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Running gromacs 4.6.5 on BGQ
Hi, I installed the newest version of gromacs on BGQ: I used these options for whole installation cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$HOME/gromacs-4.6.5/ -DGMX_DOUBLE=ON -DCMAKE_PREFIX_PATH=$HOME/fftw/ .. and this option for mdrun installation: cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$HOME/gromacs-4.6.5/ -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-CXX -DGMX_DOUBLE=ON -DCMAKE_PREFIX_PATH=$HOME/fftw/ .. And it installed without errors. But, whenever I try to run any gromacs tool both on access node or in the queue I always end up with this error: /bgsys/source/srcV1R2M0.3103/comm/sys/buildtools/pami/common/bgq/BgqPersonality.h:102: /bgsys/source/srcV1R2M0.3103/comm/sys/buildtools/pami/common/bgq/BgqPersonality.h<102> Abort I tried to install with and without static links but it does not help much... I use gcc 4.4.6 and XL 12.1.0 Any ideas? Thank you. Best, tomek -- View this message in context: http://gromacs.5086.x6.nabble.com/Running-gromacs-4-6-5-on-BGQ-tp5013297.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Acpype charge
Dear GMX Users I 'm running MD Simulation between DNA-ligand interaction using parmbsc0 force field. I use ACPYPE tool for calculation of the lignad topologies and other parameters. Is the charge in the itp file achieved from ACPYPE reliable? or Should it be reassign? Best Regards -- 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] Acpype charge
I would suggest you to read the acpype paper http://www.biomedcentral.com/1756-0500/5/367 and the references within. Alan On 12 December 2013 19:37, kiana moghaddam wrote: > Dear GMX Users > > I 'm running MD Simulation between DNA-ligand interaction using parmbsc0 > force field. I use ACPYPE tool for calculation of the lignad topologies > and other parameters. Is the charge in the itp file achieved from ACPYPE > reliable? or Should it be reassign? > > Best Regards > -- > 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. > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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] Pressure coupling constants
Hi Thanks a lot. But if one wants to simulate the sudden expansion (in a crude way ,of course) smaller coupling constant would be more appropriate. Isn't it? santo - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA -- View this message in context: http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013300.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Running gromacs 4.6.5 on BGQ
Compiling a functional BG/Q installation of GROMACS requires using two different compilers. Your first installation has MPI, which is not useful for the tools (see http://www.gromacs.org/Documentation/Installation_Instructions#5.3.2._BlueGene.2fQ), and (apparently, from your symptoms) the XL compiler for the back end, not gcc for the front end. See your-build-dir/src/buildinfo.h to confirm. You will need to consult your local documentation for how to set up your environment to use the recommended front-end compiler, so that a new run of cmake will detect it. Mark On Fri, Dec 13, 2013 at 6:24 AM, didymos wrote: > Hi, > > I installed the newest version of gromacs on BGQ: > I used these options for whole installation > cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$HOME/gromacs-4.6.5/ > -DGMX_DOUBLE=ON -DCMAKE_PREFIX_PATH=$HOME/fftw/ .. > > > and this option for mdrun installation: > cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$HOME/gromacs-4.6.5/ > -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-CXX -DGMX_DOUBLE=ON > -DCMAKE_PREFIX_PATH=$HOME/fftw/ .. > > > And it installed without errors. > But, whenever I try to run any gromacs tool both on access node or in the > queue I always end up with this error: > > > /bgsys/source/srcV1R2M0.3103/comm/sys/buildtools/pami/common/bgq/BgqPersonality.h:102: > > /bgsys/source/srcV1R2M0.3103/comm/sys/buildtools/pami/common/bgq/BgqPersonality.h<102> > Abort > > I tried to install with and without static links but it does not help > much... > I use gcc 4.4.6 and XL 12.1.0 > Any ideas? > Thank you. > Best, > > tomek > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Running-gromacs-4-6-5-on-BGQ-tp5013297.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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.
Re: [gmx-users] Pressure coupling constants
The most physical thing would be to prepare a system in a small NVT box, then make the box bigger along one dimension, then do an NVT simulation of that system and see what happens along that dimension over time. Barostats are simply not designed to do nonequilibrium right. They magically create volume at all points in the box simultaneously. An equilibrium simulation doesn't care where in the box the volume appears; a nonequilibrium simulation very much does. On Thu, Dec 12, 2013 at 4:01 PM, kpsanto wrote: > Hi > Thanks a lot. But if one wants to simulate the sudden expansion (in a crude > way ,of course) smaller coupling constant would be more appropriate. Isn't > it? > > santo > > - > K. P. Santo > Post doctoral fellow > Department of Chemistry > University of North Carolina at Chapel Hill > Chapel Hill, NC, USA > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013300.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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.
Re: [gmx-users] OPLS force field parameters
On Thu, Dec 12, 2013 at 12:45 PM, Ehsan Sadeghi wrote: > Hi gmx users, > > I try to use OPLS force field for my simulation. I added the following > residue to the aminoacids.rtp, but when I generate the topol.top file it > does not show the the bond stretching, angle bond, dihedrals. > > > [ NAF ] >[ atoms ] > C1opls_966 0.3846 1 > C2opls_966 0.3846 1 > C3opls_966 0.3846 1 > C4opls_966 0.3846 1 > F17 opls_972 -0.1923 1 > F18 opls_972 -0.1923 1 > F19 opls_972 -0.1923 1 > F20 opls_972 -0.1923 1 > F21 opls_972 -0.1923 1 > F22 opls_972 -0.1923 1 > F23 opls_972 -0.1923 1 > F24 opls_972 -0.1923 1 > C5opls_966 0.3846 1 > C6opls_966 0.3846 1 > C7opls_966 0.3846 1 > C8opls_966 0.3846 1 > F25 opls_972 -0.1923 1 > F26 opls_972 -0.1923 1 > F27 opls_972 -0.1923 1 > F28 opls_972 -0.1923 1 > F29 opls_972 -0.1923 1 > F30 opls_972 -0.1923 1 > F31 opls_972 -0.1923 1 > F32 opls_972 -0.1923 1 > C9opls_966 0.3846 1 > C10 opls_966 0.3846 1 > C11 opls_966 0.3846 1 > C12 opls_966 0.3846 1 > F33 opls_972 -0.1923 1 > F34 opls_972 -0.1923 1 > F35 opls_972 -0.1923 1 > F36 opls_972 -0.1923 1 > F37 opls_972 -0.1923 1 > F38 opls_972 -0.1923 1 > F39 opls_972 -0.1923 1 > F40 opls_972 -0.1923 1 > C13 opls_966 0.3846 1 > C14 opls_966 0.3846 1 > C15 opls_967 0.3218 1 > C16 opls_966 0.3846 1 > F41 opls_972 -0.1923 1 > F42 opls_972 -0.1923 1 > F43 opls_972 -0.1923 1 > F44 opls_972 -0.1923 1 > F45 opls_973 -0.1641 1 > F46 opls_972 -0.1923 1 > F47 opls_972 -0.1923 1 > C48 opls_968 0.3228 1 > O49 opls_980 -0.2742 1 > C50 opls_969 0.401 1 > O51 opls_981 -0.2604 1 > C52 opls_967 0.3218 1 > C53 opls_971 0.3216 1 > F55 opls_974 -0.1637 1 > F56 opls_974 -0.1637 1 > F57 opls_975 -0.1932 1 > C58 opls_970 0.4947 1 > F59 opls_977 -0.1662 1 > F60 opls_977 -0.1662 1 > F61 opls_978 -0.3278 1 > F62 opls_978 -0.3278 1 > F66 opls_976 -0.1649 1 > F67 opls_976 -0.1649 1 > F68 opls_976 -0.1649 1 > S54 opls_979 1.4124 1 > O63 opls_982 -0.632 1 > O64 opls_982 -0.632 1 > O65 opls_982 -0.632 1 > Note that assigning all atoms to a single charge group is inappropriate. Surely grompp will warn about this, but you should construct the groups more carefully. > However, the parameters that we had in topol file are different: > > [ bonds ] > ; aiaj functc0c1c2c3 > 1 2 1 > 1 5 1 > > [ angles ] > ; aiajak functc0c1c2 >c3 > 2 1 5 1 > 2 1 6 1 > 5 1 6 1 > > > How gromacs can find c0, c1,c2 and c3 from b0, kb, th0, and cth in the > ffbonded.itp? > > I answered this already: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-December/086118.html You provide the parameters in ffbonded.itp, grompp goes and finds them. If something is missing, grompp fails. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] Pressure coupling constants
guess that right! but why do you think NVT scaling of velocities is physical which should also affect the non-equilibrium expansion process? thanks in advance Santo - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA -- View this message in context: http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013303.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Pressure coupling constants
You're right, NVE would probably be better! Otherwise, you would not get expansionary cooling. On Thu, Dec 12, 2013 at 7:08 PM, kpsanto wrote: > guess that right! but why do you think NVT scaling of velocities is physical > which should also affect the non-equilibrium expansion process? > > thanks in advance > Santo > > - > K. P. Santo > Post doctoral fellow > Department of Chemistry > University of North Carolina at Chapel Hill > Chapel Hill, NC, USA > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013303.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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.
