[gmx-users] The PMF curve is asymmetric (However many results of membrane penetration are symmetric)
Hi all: I tried to use MD simulation to pull a drug across the POPC membrane and to calculate PMF. I obtained the PMF curve following the guide (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/) I found the PMF curve increases as the penetration process proceeds. The PMF curve is asymmetric, it increases in the whole time. However many results of membrane penetration are symmetric, e.g. increase earlier and decrease lately (X=0 in the central) . How can I get the similar result? There are examples of this in the GROMACS manual (see, e.g. the diagram for the cylinder geometry in the case of layered systems), but it is too difficult for me to understand it. I also read the answer (https://www.researchgate.net/post/How_to_pull_a_solute_across_liquid-liquid_interface). I am sure that a drug and a membrane will come closer when I used the negative pull rate. But I have some doubts whether the drug can continue to move ahead and leave the membrane after it arrive at the central of membrane. Best regards, Best regards, 祝 安好 -- Guodong YE Ph.D, Professor Department of Pharmaceutical Chemistry School of Pharmaceutical Sciences Guangzhou Medical University Address: Guangzhou Medical University (Panyu Campus) Xinzao Town, Panyu District, Guangzhou, China, 511436 -- 叶国东,博士,教授 广州医科大学 药学院 化学教研室 广州市番禺区新造镇 -- 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] PROBLEM IN COORDINATES
thanks. problem resolved. On 21 Feb 2018 08:13, "Justin Lemkul" wrote: > > > On 2/20/18 9:50 PM, neelam wafa wrote: > >> Dear gmx users >> >> I am still stuck at this point. >> error obtained is this >> Fatal error: >> number of coordinates in coordinate file (solv.gro, 32803) >> does not match topology (topol.top, 32818) >> There is a difference of 15. I think its not considering the ligand as 15 >> is i think for ligand. the ligand. the entries of ligand in gro file are >> these. >> 15 >> 1JZ4 C4 1 2.946 -2.601 0.141 >> 1JZ4 C14 2 3.009 -2.568 0.005 >> 1JZ4 C13 3 2.965 -2.664 -0.107 >> 1JZ4 C12 4 2.834 -2.642 -0.154 >> 1JZ4 C11 5 2.734 -2.734 -0.116 >> 1JZ4 H11 6 2.753 -2.810 -0.040 >> 1JZ4 C7 7 2.606 -2.727 -0.176 >> 1JZ4 H7 8 2.529 -2.798 -0.147 >> 1JZ4 C8 9 2.578 -2.628 -0.273 >> 1JZ4 H8 10 2.479 -2.624 -0.319 >> 1JZ4 C9 11 2.677 -2.536 -0.311 >> 1JZ4 H9 12 2.655 -2.460 -0.387 >> 1JZ4 C10 13 2.804 -2.543 -0.251 >> 1JZ4 OAB 14 2.900 -2.451 -0.285 >> 1JZ4 HAB 15 2.863 -2.389 -0.354 >> 0.68000 0.68000 0.68000 >> >> Help me out please. >> > > Looks like you probably didn't copy the ligand coordinates into the > topology. The topology thinks it's there and the coordinates say it's not. > The solution to this error is always the same: proper bookkeeping. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] selection of the type of box in molecular dynamics in GROMACS
Hi everyone, I want to know that on what basis we have to select the specific type of a box for a particular protein during molecular dynamics in GROMACS ? Thank you in advance. -- Thanks & Regards, VIKRAM DALAL Research Scholar -- 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] query about coul-SR
Thanks for your reply Alex. On 23 February 2018 at 02:01, Alex wrote: > No, this is the particle-particle cutoff portion in the particle-particle > + particle-mesh scheme. Unless the size of your entire protein is smaller > than rcoulomb. > > Alex > > > On 2/22/2018 1:07 PM, Saumyak Mukherjee wrote: > >> Dear Users, >> >> In the output of gmx energy, coul-SR means short range Coulomb >> interactions. So if I have coul-SR for a protein, does it give the total >> self-interaction energy (Coulomb) of the protein? >> >> Any help is much appreciated. >> >> Thanks & regards, >> >> *Saumyak Mukherjee* >> >> Senior Research Fellow, >> Prof. Biman Bagchi's Lab, >> Solid State and Structural Chemistry Unit, >> Indian Institute of Science, >> Bangalore - 560012, >> Karnataka, India. >> >> >> >> >> >> >> > > -- > 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. -- Thanks & regards, *Saumyak Mukherjee* Senior Research Fellow, Prof. Biman Bagchi's Lab, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore - 560012, Karnataka, India. -- 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] query about coul-SR
No, this is the particle-particle cutoff portion in the particle-particle + particle-mesh scheme. Unless the size of your entire protein is smaller than rcoulomb. Alex On 2/22/2018 1:07 PM, Saumyak Mukherjee wrote: Dear Users, In the output of gmx energy, coul-SR means short range Coulomb interactions. So if I have coul-SR for a protein, does it give the total self-interaction energy (Coulomb) of the protein? Any help is much appreciated. Thanks & regards, *Saumyak Mukherjee* Senior Research Fellow, Prof. Biman Bagchi's Lab, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore - 560012, Karnataka, India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] query about coul-SR
Dear Users, In the output of gmx energy, coul-SR means short range Coulomb interactions. So if I have coul-SR for a protein, does it give the total self-interaction energy (Coulomb) of the protein? Any help is much appreciated. Thanks & regards, *Saumyak Mukherjee* Senior Research Fellow, Prof. Biman Bagchi's Lab, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore - 560012, Karnataka, India. -- 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] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?
Dear Gromacs, The scount.xvg file was obtained after running echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns The secondary structures listed are: 'Structure','Coil','B-Sheet','B-Bridge','Bend','Turn','A-Helix','3-Helix','5-Helix' I ran the command for different proteins. It surprised me that the last '5-Helix' randomly displayed in the scount.xvg. Maybe some proteins did not have the '5-Helix', but why not just show them as 0? Can this be improved? Because I am using a script to read the scount.xvg files, so I want all the files have the same format. Thank you. Yours sincerely Cheng -- 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] Example of arithmetic expression in gmx select?
Hi all, I'm trying to do selections that require addition, which is supposed to be supported according to 'gmx help selections'. I get syntax error however when doing from within 'gmx select': a=1+1 resid a What is the right syntax for achieving a=2...? Thanks, Viveca -- 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] calculating force for a restrained structure
Dear Justin and all GROMACS users, I'm simulating a nano tube which is placed in a lipid system. the nano tube is completely restrained to halt rotation or COM movement. Now, I intend to calculate the force applied from lipid layer to nanotube. the question is how can i eliminate the effect of spring force from restraining option? can i extract the force of a specific group from the net force applied to nanotube? Thank you for any help, Ali -- 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] problems with the output of pullx
Hi, I am using gromacs to get the PMF of a peptide of about 20 amino acids, moving inside of a bilayer membrane. After pulling the peptide inside the membrane now I am using pull-coord1-type = umbrella and pull-coord1-geometry = distance to sample configurations in each window for the umbrella simulations along the z axis (axis perpendicular to the membrane surface). Runs finish ok, no error messages. The problem is that when I looked at the contents of the pullx file I observed spikes (up to 5 or more Angstroms) in the z coordinate separating the center of mass of the peptide from the membrane center. But when I extract the z coordinates of the center of mass of the two groups and compute the difference the values look reasonable with no spikes. Here an example (it starts good): time (ps) from pullx from traj analysis 20.000 0.475923002 0.475919992 200010.000 0.498394012 0.498389989 200020.000 0.527589977 0.527589977 200030.000 0.491834015 0.493739992 200040.000 0.485377997 0.485379994 200050.000 0.488474995 0.488469988 200060.000 0.507991016 0.507990003 200070.000 0.475095987 0.475100011 200080.000 0.465889990 0.465889990 200090.000 0.515878975 0.515879989 200100.000 0.501435995 0.501429975 200110.000 0.505191982 0.505190015 Here a bad section: 214000.000 0.427343011 0.601450026 214010.000 0.484564990 0.545799971 214020.000 0.530139029 0.603110015 214030.000 0.176231995 0.650319993 214040.000 0.342045009 0.637109995 214050.000 0.181202993 0.636659980 214060.000 0.338808000 0.595300019 214070.000 0.442301005 0.547529995 214080.000 0.396046013 0.565050006 214090.000 0.431407988 0.538460016 214100.000 0.402586013 0.56825 214110.000 0.438223004 0.575810015 Then good again: 23.000 0.477869004 0.477869987 230010.000 0.511840999 0.511839986 230020.000 0.469146013 0.469150007 230030.000 0.480194002 0.480190009 230040.000 0.525618017 0.525619984 230050.000 0.498955995 0.498950005 230060.000 0.489230990 0.489230007 230070.000 0.531931996 0.531930029 230080.000 0.535376012 0.535380006 230090.000 0.488822013 0.48883 230100.000 0.510704994 0.510699987 230110.000 0.524537981 0.524540007 230120.000 0.513199985 0.513189971 This problem happens in most umbrella windows that I have examined, sometimes several times during the long trajectories I am running. The pullf output also have those spikes. Here is the mdp file I am using: integrator = md dt = 0.002 nsteps = 5000 nstlog = 1 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstcalcenergy = 500 nstenergy = 500 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; tcoupl = Nose-Hoover tc_grps = PROT MEMB SOL_ION tau_t = 1.01.01.0 ref_t = 303.15 303.15 303.15 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 500 comm_mode = linear comm_grps = PROT_MEMB SOL_ION ; refcoord_scaling= com ; pull= yes pull-coord1-type= umbrella pull-coord1-geometry= distance pull-coord1-dim = N N Y pull-ngroups= 2 pull-ncoords= 1 pull-coord1-groups = 1 2 pull-group1-name= MEMB pull-group2-name= PROT pull-coord1-init= 0.400 pull-coord1-k = 1000; kJ mol^-1 nm^-2 pull-nstxout= 500; every 1 ps pull-nstfout= 500; every 1 ps I am not sure what is wrong here. It seems a bug to me. Here is the header of the log file: Log file opened on Thu Feb 15 11:09:05 2018 Host: sb202 pid: 254782 rank ID: 0 number of ranks: 112 :-) GROMACS - mdrun_mpi, 2016.4 (-: GROMACS: mdrun_mpi, version 2016
Re: [gmx-users] New in the mailing list
Hi, Use the same version of GROMACS for converting the tpr as you used for running the simulation. Old code can't know about new modules, etc. Mark On Thu, Feb 22, 2018, 14:37 Giordano Perini wrote: > Hello everyone, > I've just joined this mailing list in order to understand how to solve a > problem while extending a simulation. I am trying to generate a new tpr > file via command line: > > gmx convert-tpr -s [old].tpr -extend [timeneeded] -o new.tpr > > BUT, when compiling, it tells me: > > reading tpx file (md_0_1.tpr) version 110 with version 103 program > > What can I do to solve that "fatal error"? > > Thank you for your kindness, > Giordano Perini, PhD student, Institute of Physics, Catholic University of > Sacred Heart, Rome. > -- > 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] New in the mailing list
Hello everyone, I've just joined this mailing list in order to understand how to solve a problem while extending a simulation. I am trying to generate a new tpr file via command line: gmx convert-tpr -s [old].tpr -extend [timeneeded] -o new.tpr BUT, when compiling, it tells me: reading tpx file (md_0_1.tpr) version 110 with version 103 program What can I do to solve that "fatal error"? Thank you for your kindness, Giordano Perini, PhD student, Institute of Physics, Catholic University of Sacred Heart, Rome. -- 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.