[gmx-users] System shrinkage during vacuum simulation
Hello everyone, I ran a short MD simulation with a 3dc ewald geometry to simulate a vacuum slab at the top and bottom of my bilayer system. I equilibrated my system, tripled the size of my system in the z-direction and then added the 3dc geometry. My mdp script is written as below: title = Production MD ; Run parameters integrator = md nsteps = 2500 dt= 0.002 ; Output control nstxout = 2000 nstvout = 2000 nstxtcout = 2000 nstenergy = 2000 nstlog = 2000 ; Bond parameters continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb = 1.6 rvdw = 1.6 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = Nose-Hoover tc-grps = System tau_t = 0.2 ref_t = 310 ; EWALD/PME/PPPM parameters = ewald-geometry: 3dc ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc= xyz ; Dispersion correction DispCorr = EnerPres ; Velocity generation gen_vel = no My system shrunk down to a value close to the original dimension in the z direction as soon as the simulation started after I analyzed it using g_energy. Is there a mistake with my production .mdp file? I will truly appreciate your assistance. Regards, Sanim Rahman -- 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] Plotting Density Over Time?
Hello everyone, I am curious if there is a feature in g_density that will allow me to calculate the density of my system at every single frame. I am hoping to track density change over time to calculate membrane thickness (peak to peak of electron density profile) and its standard deviation. Regards, Sanim Rahman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GROMACS and SIMtoEXP
Thank you David, I realized my mistake and I need to be using number density when working with SIMtoEXP however, I was wondering if there is some script out there to easily convert my number density from gromacs to the compatible file format for SIMtoEXP. Regards, Sanim Rahman On Wed, Jun 21, 2017 at 2:02 AM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 20/06/17 23:16, Sanim Rahman wrote: > >> Hello Everyone, >> >> I am interested in using the SIMtoEXP program to directly compare my >> simulation results to experimental values. The program only can process >> electron density profiles written as .dat and .sim files. >> >> Is anyone aware of scripts or GROMACS options that will allow me to output >> my electron density profile into a .dat or .sim file that can be processed >> by SIMtoEXP? >> >> Regards, >> Sanim Rahman >> >> You have the wrong program if you need electron densities. > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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] Using PME with Slab Boundaries
Hello, I was attempting to run an equilibration on my system that has slab boundaries. I am using 3dc Ewald Geometry and PME. I am also using PBC in the x,y,z dimensions. During grompp, I received the following warning: *WARNING: With PME and ewald_geometry = 3dc you should use pbc = xy* I have seen simulations using PBC in all three dimensions with slab boundaries with PME. What are the consequences of running a simulation with slab geometry and pbc in all three dimensions with PME? Regards, Sanim Rahman -- 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] Technqiues for Applying Assymmetric Ion Concentrations?
Hello Users, I am planning to do a bilayer simulation with asymmetric ion concentrations using slab boundaries. I am trying to modify the concentration of each ionic species on each side of the bilayer, however, I am struggling to find a technique that will allow me to effectively manipulate the concentrations of each side of the bilayer. Are there any suggestions on how to do this? I would imagine splitting the system in half at the hydrophobic core and then using the genion command for each half would do the trick but I am unaware of any commands that will allow me to split the system as such. The membrane system that I am using is from CHARMM-GUI. I will truly appreciate your input. Regards, Sanim Rahman -- 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] Deuterium Order Parameter Calculations
Thank you Justin, That makes much more sense. I was able to fix the error. I have one more question that is out of topic from the original question. Is there a guide that informs the user on what index groups should be made for each type of analysis? I am also trying to use gmx_potential to do electrostatic potential on a membrane solvated in KCl. If I want to do this, what index group would I use? Regards, Sanim Rahman On Tue, May 30, 2017 at 8:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/30/17 7:16 PM, Sanim Rahman wrote: > >> Hello everyone, >> >> I have a question about calculating Deuterium Order Parameters using >> g_order. Is it common to get unrealistic values for Scd if you have not >> run >> the simulation long enough (over 25 ns?)? I ran the calculations after >> equilibration on a POPC bilayer just to experiment with the command and I >> received "NaN" values for two of my carbons for my calculations on Sn1. >> >> > This means something is wrong with your inputs, likely incorrectly > specified index groups. > > -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. > -- 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] Deuterium Order Parameter Calculations
Hello everyone, I have a question about calculating Deuterium Order Parameters using g_order. Is it common to get unrealistic values for Scd if you have not run the simulation long enough (over 25 ns?)? I ran the calculations after equilibration on a POPC bilayer just to experiment with the command and I received "NaN" values for two of my carbons for my calculations on Sn1. I will truly appreciate your response and assistance. Regards, Sanim Rahman *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017 Co-Founder and Co-President of the Undergraduate Research Society Research Assistant, Bhethanabotla-Frisina Neural Plasmonics Stimulation Group <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> -- 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] Deuterium Order Parameter Analysis
Hello everyone, I have a question about calculating Deuterium Order Parameters using g_order. Is it common to get unrealistic values for Scd if you have not run the simulation long enough (over 25 ns?)? I ran the calculations after equilibration just to experiment with the command and I received "NaN" values for two of my carbons for my calculations on Sn1. I will truly appreciate your response and assistance. Regards, Sanim Rahman -- 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] (no subject)
Hi Justin, I completely dazed over the "download .tgz" option at the top right of the screen. I got all of the files I need for my membrane. Thank you! *Sanim Rahman* On Sat, Mar 18, 2017 at 8:03 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/18/17 1:25 AM, Sanim Rahman wrote: > >> Sorry I found this thread here: >> >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users >> /2016-September/108197.html >> >> >> From my understanding, I use pdb2gmx on my entire output file, however, >> where does the data in the .psf file go? >> >> > You shouldn't be using pdb2gmx at all. CHARMM-GUI gives you a complete > system topology that should work, as long as you don't modify anything > about the system. > > -Justin > > > *Sanim Rahman* >> B.S. Chemical Engineering, 2019 >> Resident Assistant, Castor Hall Engineering Living Learning Community >> 2016-2017 >> Co-Founder and Co-President of the Undergraduate Research Society >> Undergraduate Researcher, Global Center for Hearing and Speech Research >> <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> >> >> >> On Sat, Mar 18, 2017 at 12:37 AM, Sanim Rahman <san...@mail.usf.edu> >> wrote: >> >> Hi all, >>> >>> I am trying to run grompp on POPC lipid bilayer that I constructed in >>> CHARMM-GUI. I originally input the whole assembled bilayer from >>> CHARMM-GUI, >>> however, I received the error: >>> >>> "No Default U-B Types" >>> >>> From a few previous threads, it was suggested that I stripped the waters >>> and use pdb2gmx on them separately in GROMACS. I did that and included >>> the >>> #include command in my lipid topology file to reference water.itp. >>> However, >>> I receive the following error: >>> >>> "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr >>> = >>> 1, >>> while at->nr = 17152)" >>> >>> This is what the end of my POPC topology file looks like: >>> >>> *; Include Position restraint file* >>> *#ifdef POSRES* >>> *#include "posre.itp"* >>> *#endif* >>> >>> *; Include water chain topology* >>> *#include "water.itp"* >>> >>> *; Include water topology* >>> *#include "./charmm36-nov2016.ff/tip3p.itp"* >>> >>> *#ifdef POSRES_WATER* >>> *; Position restraint for each water oxygen* >>> *[ position_restraints ]* >>> *; i funct fcx fcyfcz* >>> * 11 1000 1000 1000* >>> *#endif* >>> >>> *; Include topology for ions* >>> *#include "./charmm36-nov2016.ff/ions.itp"* >>> >>> *[ system ]* >>> *; Name* >>> *Protein* >>> >>> *[ molecules ]* >>> *; Compound#mols* >>> *Other 1* >>> *Water 1* >>> >>> I recalled implementing the same technique in one of the GROMACS >>> tutorials, >>> but I am unsure what I am doing differently in my approach to receive >>> this >>> error. >>> Thank you. I will truly appreciate your assistance. >>> *Sanim Rahman* >>> B.S. Chemical Engineering, 2019 >>> Resident Assistant, Castor Hall Engineering Living Learning Community >>> 2016-2017 >>> Co-Founder and Co-President of the Undergraduate Research Society >>> Undergraduate Researcher, Global Center for Hearing and Speech Research >>> <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> >>> -- >>> 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. > -- 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] (no subject)
Sorry I found this thread here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108197.html >From my understanding, I use pdb2gmx on my entire output file, however, where does the data in the .psf file go? *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017 Co-Founder and Co-President of the Undergraduate Research Society Undergraduate Researcher, Global Center for Hearing and Speech Research <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> On Sat, Mar 18, 2017 at 12:37 AM, Sanim Rahman <san...@mail.usf.edu> wrote: > Hi all, > > I am trying to run grompp on POPC lipid bilayer that I constructed in > CHARMM-GUI. I originally input the whole assembled bilayer from CHARMM-GUI, > however, I received the error: > > "No Default U-B Types" > > From a few previous threads, it was suggested that I stripped the waters > and use pdb2gmx on them separately in GROMACS. I did that and included the > #include command in my lipid topology file to reference water.itp. However, > I receive the following error: > > "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = > 1, > while at->nr = 17152)" > > This is what the end of my POPC topology file looks like: > > *; Include Position restraint file* > *#ifdef POSRES* > *#include "posre.itp"* > *#endif* > > *; Include water chain topology* > *#include "water.itp"* > > *; Include water topology* > *#include "./charmm36-nov2016.ff/tip3p.itp"* > > *#ifdef POSRES_WATER* > *; Position restraint for each water oxygen* > *[ position_restraints ]* > *; i funct fcxfcyfcz* > * 11 1000 1000 1000* > *#endif* > > *; Include topology for ions* > *#include "./charmm36-nov2016.ff/ions.itp"* > > *[ system ]* > *; Name* > *Protein* > > *[ molecules ]* > *; Compound#mols* > *Other 1* > *Water 1* > > I recalled implementing the same technique in one of the GROMACS tutorials, > but I am unsure what I am doing differently in my approach to receive this > error. > Thank you. I will truly appreciate your assistance. > *Sanim Rahman* > B.S. Chemical Engineering, 2019 > Resident Assistant, Castor Hall Engineering Living Learning Community > 2016-2017 > Co-Founder and Co-President of the Undergraduate Research Society > Undergraduate Researcher, Global Center for Hearing and Speech Research > <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> > -- > 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] (no subject)
Hi all, I am trying to run grompp on POPC lipid bilayer that I constructed in CHARMM-GUI. I originally input the whole assembled bilayer from CHARMM-GUI, however, I received the error: "No Default U-B Types" >From a few previous threads, it was suggested that I stripped the waters and use pdb2gmx on them separately in GROMACS. I did that and included the #include command in my lipid topology file to reference water.itp. However, I receive the following error: "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr = 17152)" This is what the end of my POPC topology file looks like: *; Include Position restraint file* *#ifdef POSRES* *#include "posre.itp"* *#endif* *; Include water chain topology* *#include "water.itp"* *; Include water topology* *#include "./charmm36-nov2016.ff/tip3p.itp"* *#ifdef POSRES_WATER* *; Position restraint for each water oxygen* *[ position_restraints ]* *; i funct fcxfcyfcz* * 11 1000 1000 1000* *#endif* *; Include topology for ions* *#include "./charmm36-nov2016.ff/ions.itp"* *[ system ]* *; Name* *Protein* *[ molecules ]* *; Compound#mols* *Other 1* *Water 1* I recalled implementing the same technique in one of the GROMACS tutorials, but I am unsure what I am doing differently in my approach to receive this error. Thank you. I will truly appreciate your assistance. *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017 Co-Founder and Co-President of the Undergraduate Research Society Undergraduate Researcher, Global Center for Hearing and Speech Research <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> -- 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 Defaults Error Due to Force Field Mixing
Hi all, I am attempting to run a membrane protein simulation where I am describing my protein and solvent in terms of CHARMM27 and my lipids in CHARMM36. When I use the grompp command, I get the following error: Fatal error: Syntax error - File forcefield.itp, line 9 Last line read: '[ defaults ]' Invalid order for directive defaults To create my topology file, I took my protein.top and at the bottom included my lipid.itp and solvent.itp. The error is referencing to my charmm36 force field file. I was unsure what to do so I just removed the line with [ defaults ] on it and tried running it again. This time I received this error: Fatal error: Syntax error - File ffnonbonded.itp, line 5 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Is the source of the error from how my topology files are processing the force field files since I am using both CHARMM27 and CHARMM36? I read a previous thread that you can't have two [ default ] lines which make sense but I am unsure of what is the proper protocol to get around this to include both force fields. Any help will be deeply appreciated! Thank You, *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017 Co-Founder and Co-President of the Undergraduate Research Society Undergraduate Researcher, Global Center for Hearing and Speech Research -- 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] GRO File Merging
Hello Mark, I was able to get around the issue so no worries. The reason why I split them up because I wanted to describe my lipids in CHARMM36 parameters and protein in CHARMM27 in order to replicate a simulation. However, is my thought process for the topology file correct? Regards, *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017 Co-Founder and Co-President of the Undergraduate Research Society Undergraduate Researcher, Global Center for Hearing and Speech Research <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> On Sat, Feb 25, 2017 at 2:59 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Why are you splitting things up? The whole coordinate file from charmm gui > is the useful thing. > > Mark > > On Sat, 25 Feb 2017 20:21 Sanim Rahman <san...@mail.usf.edu> wrote: > > > Hi all, > > > > I have been using gromacs to design a membrane protein system. I used > > CHARMM-GUI to design my membrane and then was able to split my system > into > > three parts (protein, lipid, solvent) and convert it into .gro format. I > am > > able to individually view each part in VMD all together but when I use: > > > > *cat protein.gro lipid.gro solvent.gro > system.gro* > > > > The molecule does not show up in VMD. I properly edit the number of atoms > > and the box coordinates of the system by using -editconf to correct the > box > > coordinates. I receive no errors in VMD as well. What should I do to fix > > this? > > > > Also when combining topology files, I would convert lipid.top and > > solvent.top into .itp files and use the #include statement to combine > them > > into my protein.top file? After that, my system should be set correct? > > > > Thank You, > > Sanim Rahman > > -- > > 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.
[gmx-users] GRO File Merging
Hi all, I have been using gromacs to design a membrane protein system. I used CHARMM-GUI to design my membrane and then was able to split my system into three parts (protein, lipid, solvent) and convert it into .gro format. I am able to individually view each part in VMD all together but when I use: *cat protein.gro lipid.gro solvent.gro > system.gro* The molecule does not show up in VMD. I properly edit the number of atoms and the box coordinates of the system by using -editconf to correct the box coordinates. I receive no errors in VMD as well. What should I do to fix this? Also when combining topology files, I would convert lipid.top and solvent.top into .itp files and use the #include statement to combine them into my protein.top file? After that, my system should be set correct? Thank You, Sanim Rahman -- 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] Issues combining protein and membrane file?
My apologies, I sent you the wrong file. Here is the right one. I made the edits and all the atoms are properly accounted for in VMD but they are not visible. Also when I used the inflategro script on it, only 148 atoms were read. Here is the command I used: perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat Here are the files I attached: Original- https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 Inflated- https://www.dropbox.com/s/aiu89i1n5nj5bpp/system_inflated.gro?dl=0 Regards, Sanim Rahman On Sat, Feb 18, 2017 at 7:22 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/18/17 6:55 PM, Sanim Rahman wrote: > >> Thank you Justin, >> >> I was able to remove the velocities from my file but it still fails to >> read. I attached a dropbox link to my file if you have the time to take a >> look at it. >> >> https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 >> >> > The file needs a title line. The number of atoms must be the second line, > not the first. > > http://manual.gromacs.org/documentation/2016.2/user-guide/fi > le-formats.html#gro > > -Justin > > > Thank you! >> >> Regards, >> Sanim Rahman >> >> >> On Sat, Feb 18, 2017 at 5:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 2/18/17 4:46 PM, Sanim Rahman wrote: >>> >>> Hi all, >>>> >>>> I am trying to prepare a system for a MD simulation of an ion channel >>>> (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein >>>> into >>>> the lipid membrane. I am currently trying the inflategro.pl approach >>>> done >>>> in the KALP15 tutorial. The first step with the prepared structural >>>> files >>>> was to combine them together using >>>> >>>> cat protein.gro lipid.gro > system.gro >>>> >>>> However, after combining them and loading them into VMD, my system has >>>> become distorted and only 151 atoms out 90131 atoms were read. Is there >>>> anything I can do to fix this issue? >>>> >>>> I believe it may have to do with the nomenclature of my script. The .gro >>>> file for my protein and lipid bilayer is not written in a consistent >>>> format: >>>> >>>> 421THR CA10936 4.791 7.926 7.910 >>>> 421THR CB10937 4.822 7.797 7.831 >>>> 421THROG110938 4.862 7.831 7.698 >>>> 421THRHG110939 4.882 7.748 7.647 >>>> 421THRCG210940 4.701 7.705 7.826 >>>> 421THR C10941 4.754 7.892 8.055 >>>> 421THR O110942 4.772 7.974 8.146 >>>> 421THR O210943 4.649 7.808 8.074 >>>> 1POPCC11 5.168 4.220 4.016 -0.2491 0.0715 0.4836 >>>> 1POPCC22 4.942 4.276 3.936 0.1967 0.1087 -0.5850 >>>> 1POPCC33 5.108 4.444 3.993 0.3211 0.0553 -0.2150 >>>> 1POPCN44 5.085 4.311 3.935 0.2251 0.0126 -0.0777 >>>> 1POPCC55 5.129 4.301 3.795 -0.0894 -0.4945 -0.1460 >>>> 1POPCC66 5.280 4.304 3.767 0.0019 -0.2403 0.3568 >>>> 1POPC OS77 5.354 4.422 3.799 0.0579 -0.0618 -0.4147 >>>> 1POPCP88 5.512 4.403 3.778 0.1576 0.2198 0.0575 >>>> 1POPC OM99 5.532 4.289 3.686 0.1757 -0.1049 0.4662 >>>> 1POPC OM10 10 5.597 4.524 3.785 0.1671 0.2024 0.2449 >>>> 1POPC OS11 11 5.526 4.331 3.921 0.4792 -0.0093 -0.0879 >>>> >>>> >>>> VMD is probably choking on the fact that some of your lines have >>> velocity >>> information (the lipids) and others (the protein) don't. Try stripping >>> the >>> velocities and appending just the coordinates. >>> >>> I updated the number of atoms in my system and removed nonessential lines >>> >>>> as well. Also, would the inflategro procedure be appropriate for this >>>> simulation considering that I am inserting a +10,000 atom protein into a >>>> lipid membrane? >>>> >>>> >>>> Sure, we've done it with big systems, though the script is a bit of a >>> memory hog, IIRC. Haven't used it in a while. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein
Re: [gmx-users] Issues combining protein and membrane file?
Thank you Justin, I was able to remove the velocities from my file but it still fails to read. I attached a dropbox link to my file if you have the time to take a look at it. https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 Thank you! Regards, Sanim Rahman On Sat, Feb 18, 2017 at 5:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/18/17 4:46 PM, Sanim Rahman wrote: > >> Hi all, >> >> I am trying to prepare a system for a MD simulation of an ion channel >> (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein >> into >> the lipid membrane. I am currently trying the inflategro.pl approach done >> in the KALP15 tutorial. The first step with the prepared structural files >> was to combine them together using >> >> cat protein.gro lipid.gro > system.gro >> >> However, after combining them and loading them into VMD, my system has >> become distorted and only 151 atoms out 90131 atoms were read. Is there >> anything I can do to fix this issue? >> >> I believe it may have to do with the nomenclature of my script. The .gro >> file for my protein and lipid bilayer is not written in a consistent >> format: >> >> 421THR CA10936 4.791 7.926 7.910 >> 421THR CB10937 4.822 7.797 7.831 >> 421THROG110938 4.862 7.831 7.698 >> 421THRHG110939 4.882 7.748 7.647 >> 421THRCG210940 4.701 7.705 7.826 >> 421THR C10941 4.754 7.892 8.055 >> 421THR O110942 4.772 7.974 8.146 >> 421THR O210943 4.649 7.808 8.074 >> 1POPCC11 5.168 4.220 4.016 -0.2491 0.0715 0.4836 >> 1POPCC22 4.942 4.276 3.936 0.1967 0.1087 -0.5850 >> 1POPCC33 5.108 4.444 3.993 0.3211 0.0553 -0.2150 >> 1POPCN44 5.085 4.311 3.935 0.2251 0.0126 -0.0777 >> 1POPCC55 5.129 4.301 3.795 -0.0894 -0.4945 -0.1460 >> 1POPCC66 5.280 4.304 3.767 0.0019 -0.2403 0.3568 >> 1POPC OS77 5.354 4.422 3.799 0.0579 -0.0618 -0.4147 >> 1POPCP88 5.512 4.403 3.778 0.1576 0.2198 0.0575 >> 1POPC OM99 5.532 4.289 3.686 0.1757 -0.1049 0.4662 >> 1POPC OM10 10 5.597 4.524 3.785 0.1671 0.2024 0.2449 >> 1POPC OS11 11 5.526 4.331 3.921 0.4792 -0.0093 -0.0879 >> >> > VMD is probably choking on the fact that some of your lines have velocity > information (the lipids) and others (the protein) don't. Try stripping the > velocities and appending just the coordinates. > > I updated the number of atoms in my system and removed nonessential lines >> as well. Also, would the inflategro procedure be appropriate for this >> simulation considering that I am inserting a +10,000 atom protein into a >> lipid membrane? >> >> > Sure, we've done it with big systems, though the script is a bit of a > memory hog, IIRC. Haven't used it in a while. > > -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. > -- 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] Issues combining protein and membrane file?
Hi all, I am trying to prepare a system for a MD simulation of an ion channel (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein into the lipid membrane. I am currently trying the inflategro.pl approach done in the KALP15 tutorial. The first step with the prepared structural files was to combine them together using cat protein.gro lipid.gro > system.gro However, after combining them and loading them into VMD, my system has become distorted and only 151 atoms out 90131 atoms were read. Is there anything I can do to fix this issue? I believe it may have to do with the nomenclature of my script. The .gro file for my protein and lipid bilayer is not written in a consistent format: 421THR CA10936 4.791 7.926 7.910 421THR CB10937 4.822 7.797 7.831 421THROG110938 4.862 7.831 7.698 421THRHG110939 4.882 7.748 7.647 421THRCG210940 4.701 7.705 7.826 421THR C10941 4.754 7.892 8.055 421THR O110942 4.772 7.974 8.146 421THR O210943 4.649 7.808 8.074 1POPCC11 5.168 4.220 4.016 -0.2491 0.0715 0.4836 1POPCC22 4.942 4.276 3.936 0.1967 0.1087 -0.5850 1POPCC33 5.108 4.444 3.993 0.3211 0.0553 -0.2150 1POPCN44 5.085 4.311 3.935 0.2251 0.0126 -0.0777 1POPCC55 5.129 4.301 3.795 -0.0894 -0.4945 -0.1460 1POPCC66 5.280 4.304 3.767 0.0019 -0.2403 0.3568 1POPC OS77 5.354 4.422 3.799 0.0579 -0.0618 -0.4147 1POPCP88 5.512 4.403 3.778 0.1576 0.2198 0.0575 1POPC OM99 5.532 4.289 3.686 0.1757 -0.1049 0.4662 1POPC OM10 10 5.597 4.524 3.785 0.1671 0.2024 0.2449 1POPC OS11 11 5.526 4.331 3.921 0.4792 -0.0093 -0.0879 I updated the number of atoms in my system and removed nonessential lines as well. Also, would the inflategro procedure be appropriate for this simulation considering that I am inserting a +10,000 atom protein into a lipid membrane? Regards, *Sanim Rahman* -- 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] Deletion of Lipids During InflateGro?
Thank you Justin, Here are the commands I used: *gmx_mpi genconf -f popc.gro -o popc_full.gro -nbox 2 1 1* *perl inflategro.pl <http://inflategro.pl> popc_full.gro 4 POPC 1 popc_inflated.gro 5 area.dat* The first command was used to extend the length of my bilayer and the second was to inflate the structure. When I run the second command it reads that there are 128 lipids in the structure. My popc.gro originally had 128 and after using the genconf command I doubled it to 256. I checked my popc_full.gro file in VMD and opened the file in an open text editor to ensure that it was 256 lipids. I compared my popc_inflated.gro file to my popc.gro file inflated under the same parameters. They were exactly the same. Thank you for your assistance. Regards, Sanim Rahman On Fri, Dec 30, 2016 at 11:55 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/29/16 10:32 PM, Sanim Rahman wrote: > >> Dear Gromacs Users, >> >> I am working on building a lipid bilayer for my protein structure but I am >> having difficulty using the InflateGRO script. >> >> I am using a POPC bilayer and used the genconf command to extend the >> length >> of the bilayer so I would be able to go from having 128 to 256 lipids. The >> POPC bilayer I have is already converged so I plan to inflate the bilayer >> using InflateGRO, insert my protein in the center, and then converge to >> the >> appropriate lipid per area value with the script. My issue is that when I >> inflate the bilayer the script reduces the bilayer back to 128 lipids. >> >> I tried another approach by inflating my 128 lipid bilayer and then using >> the genconf command to obtain 256 lipids. However, when converging my >> bilayer, the lipids did not converge to the center of the entire system >> but >> the center of its own 128 lipid system, meaning that the bilayer split off >> into two separate pieces. >> >> Is there a way to have the script avoid reducing the number of lipids in >> the system in my original method? >> >> > Lipids will always be deleted by InflateGRO because some will overlap with > the protein. It won't delete 128 unless your protein really does occupy > 50% of the membrane area. Be sure you're using the right files as input. > If you need further help, please copy and paste your exact sequence of > commands so we can see what you're doing. > > -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. > -- 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] Deletion of Lipids During InflateGro?
Dear Gromacs Users, I am working on building a lipid bilayer for my protein structure but I am having difficulty using the InflateGRO script. I am using a POPC bilayer and used the genconf command to extend the length of the bilayer so I would be able to go from having 128 to 256 lipids. The POPC bilayer I have is already converged so I plan to inflate the bilayer using InflateGRO, insert my protein in the center, and then converge to the appropriate lipid per area value with the script. My issue is that when I inflate the bilayer the script reduces the bilayer back to 128 lipids. I tried another approach by inflating my 128 lipid bilayer and then using the genconf command to obtain 256 lipids. However, when converging my bilayer, the lipids did not converge to the center of the entire system but the center of its own 128 lipid system, meaning that the bilayer split off into two separate pieces. Is there a way to have the script avoid reducing the number of lipids in the system in my original method? I will deeply appreciate your assistance! -Sanim Rahman -- 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] Removal of Waters in Hydrophobic Core
Thank you for the responses. Here is a Dropbox link to all the files and scripts I am using: https://www.dropbox.com/sh/tk7syifmtwqmtn0/AABWwtX5XNzzBiJB08kQ-xmca?dl=0 As I mentioned before, I am working through the second tutorial of the Bevan Labs GROMACS Tutorial (KALP15 in DPPC). I am attempting to remove waters from the hydrophobic core. I attempted to remove waters from the hydrophobic core by specifying z-coordinates since the system is oriented along the z-axis. I experimented with an extreme range in the script and images I uploaded (lowerz= 5.000 upperz= 50.000). Thanks for the assistance! I deeply appreciate the time you have spent with my situation. Regards, *Sanim Rahman* B.S. Chemical Engineering, 2019 Undergraduate Researcher, Global Center for Hearing and Speech Research <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> On Mon, Nov 28, 2016 at 9:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/28/16 7:02 PM, Christopher Neale wrote: > >> You might get more help if you post your script, .gro file, images, etc. >> somewhere online and link them in a mailing list message. At this point >> it's impossible to know what is going wrong for your usage with the >> information you have posted. >> >> I don't know about Justin's scripts. Perhaps they could work together, >> but you have not said what you want to do. >> >> An alternative is simply to use good selections with "gmx select" to get >> rid of the waters inside your bilayer. >> >> > My script might be useful in this case, but only with groups derived from > what it provides. It prints index groups of the top and bottom leaflet > lipids. gmx traj -ox -com can then be used on a suitable group's P atoms > (or some other atoms within, e.g. the glycerol moiety) to determine the > upper and lower coordinate values defining the boundaries of the membrane > for removal of water. > > But gmx select would also be a good option. Probably faster, too. > > -Justin > > > ____ >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sanim >> Rahman <san...@mail.usf.edu> >> Sent: 28 November 2016 14:26:07 >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Removal of Waters in Hydrophobic Core >> >> Hey Chris, >> >> Your instruction makes much more sense. I was really confused on what was >> the point of generating the keep_these_waters.gro file initially. Thank >> you. I have noticed that water molecules were removed from my structure, >> however, it removed waters I was not looking for. It took off a random >> column of water molecules in my bilayer. What type of data file (gro, top, >> pdb, etc.) or graphical interface program is recommended to decide my >> upperz and lowerz value? >> >> I know that I am now jumping around with my questions, but are you >> familiar >> with the scripts on the site below? I believe that the >> bilayer_separator.pl >> script could complement the keepbyz.pl script perfectly. >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html >> >> Let me know if you would like me to send my current script and the image >> of >> the current model. >> >> Regards, >> >> *Sanim Rahman* >> B.S. Chemical Engineering, 2019 >> Undergraduate Researcher, Global Center for Hearing and Speech Research >> >> >> On Sat, Nov 26, 2016 at 3:36 PM, Christopher Neale < >> chris.ne...@alum.utoronto.ca> wrote: >> >> I have not run that in a long time, but looking at it (and my initial post >>> here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- >>> users/2006-May/021526.html ) it seems like I wrote out the instructions >>> incorrectly. Sorry about that! >>> >>> In the post linked above, step 8 is: >>> >>> cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro >>> >>> but I think you would really want to do this: >>> >>> cat not_last_line.gro keep_these_waters.gro last_line.gro > >>> new_system.gro >>> >>> where the change is to *actually use* the keep_these_waters.gro file that >>> we create with the script ;) >>> >>> Looks like I realized that a number of years ago: >>> http://www.mail-archive.com/gmx-users@gromacs.org/msg37736.html >>> >>> Sorry for the confusion, indeed the commands listed on the webpage seem >>> like they should lead you to recover exactly the initial file :( >>
Re: [gmx-users] Removal of Waters in Hydrophobic Core
Hey Chris,
Your instruction makes much more sense. I was really confused on what was
the point of generating the keep_these_waters.gro file initially. Thank
you. I have noticed that water molecules were removed from my structure,
however, it removed waters I was not looking for. It took off a random
column of water molecules in my bilayer. What type of data file (gro, top,
pdb, etc.) or graphical interface program is recommended to decide my
upperz and lowerz value?
I know that I am now jumping around with my questions, but are you familiar
with the scripts on the site below? I believe that the bilayer_separator.pl
script could complement the keepbyz.pl script perfectly.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html
Let me know if you would like me to send my current script and the image of
the current model.
Regards,
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Undergraduate Researcher, Global Center for Hearing and Speech Research
On Sat, Nov 26, 2016 at 3:36 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> I have not run that in a long time, but looking at it (and my initial post
> here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
> users/2006-May/021526.html ) it seems like I wrote out the instructions
> incorrectly. Sorry about that!
>
> In the post linked above, step 8 is:
>
> cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
>
> but I think you would really want to do this:
>
> cat not_last_line.gro keep_these_waters.gro last_line.gro > new_system.gro
>
> where the change is to *actually use* the keep_these_waters.gro file that
> we create with the script ;)
>
> Looks like I realized that a number of years ago:
> http://www.mail-archive.com/gmx-users@gromacs.org/msg37736.html
>
> Sorry for the confusion, indeed the commands listed on the webpage seem
> like they should lead you to recover exactly the initial file :(
>
> Note also that you need to set the upper and lower bounds correctly, and
> modify the script as noted if you are using a 4-point (or 5-ponit) water
> model, and make the noted change if your input file has also velocities.
> All of those things are correctly indicated on the webpage though.
>
> Please reply back to this list if that change works for you as expected
> and I'll bring it to Mark's attention to see if he can update the webpage.
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sanim
> Rahman <san...@mail.usf.edu>
> Sent: 26 November 2016 02:18:09
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Removal of Waters in Hydrophobic Core
>
> Thank you Chris,
>
> I tried the commands and I was able to obtain an output
> keep_these_waters.gro with about 3.5 MB of data. However, when I continued
> with the rest of the commands:
>
> tail -1 initial.gro > last_line.gro
> head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 )
> initial.gro > not_last_line.gro
> cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
> editconf -f new_system.gro -o new_system_sequential_numbers.gro
>
> I still failed to obtain a new structure. The structure is the same as
> solvated.gro. I am going to put extreme z-coordinates to see if all the
> water molecules will be removed. Other than that, do you have any
> suggestions?
>
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Undergraduate Researcher, Global Center for Hearing and Speech Research
>
>
>
> On Fri, Nov 25, 2016 at 3:48 PM, Christopher Neale <
> chris.ne...@alum.utoronto.ca> wrote:
>
> > not sure if it is a typo or perhaps a command structure I am unfamiliar
> > with, but I don't understand your command.
> >
> > Try this:
> >
> > chmod +x keepbyz.pl
> > ./keepbyz.pl new_waters.gro > keep_these_waters.gro
> >
> > see here: http://www.gromacs.org/Documentation/How-tos/
> > Membrane_Simulations?highlight=generates
> >
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sanim
> > Rahman <san...@mail.usf.edu>
> > Sent: 24 November 2016 16:12:11
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Removal of Waters in Hydrophobic Core
> >
> > Hello,
> >
> > I am currently working through the second tutorial of the Bevan Labs
> KALP15
> > simulation. I am attempting to use the keepbyz.pl script to remove the
> > waters in the hydrophobic core. I have designated a upperz and
> > lowerz coordin
Re: [gmx-users] Removal of Waters in Hydrophobic Core
Thank you Chris,
I tried the commands and I was able to obtain an output
keep_these_waters.gro with about 3.5 MB of data. However, when I continued
with the rest of the commands:
tail -1 initial.gro > last_line.gro
head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 )
initial.gro > not_last_line.gro
cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
editconf -f new_system.gro -o new_system_sequential_numbers.gro
I still failed to obtain a new structure. The structure is the same as
solvated.gro. I am going to put extreme z-coordinates to see if all the
water molecules will be removed. Other than that, do you have any
suggestions?
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Undergraduate Researcher, Global Center for Hearing and Speech Research
On Fri, Nov 25, 2016 at 3:48 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> not sure if it is a typo or perhaps a command structure I am unfamiliar
> with, but I don't understand your command.
>
> Try this:
>
> chmod +x keepbyz.pl
> ./keepbyz.pl new_waters.gro > keep_these_waters.gro
>
> see here: http://www.gromacs.org/Documentation/How-tos/
> Membrane_Simulations?highlight=generates
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sanim
> Rahman <san...@mail.usf.edu>
> Sent: 24 November 2016 16:12:11
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Removal of Waters in Hydrophobic Core
>
> Hello,
>
> I am currently working through the second tutorial of the Bevan Labs KALP15
> simulation. I am attempting to use the keepbyz.pl script to remove the
> waters in the hydrophobic core. I have designated a upperz and
> lowerz coordinated and followed the entire section highlighted in the
> instructions, however, my output (new_system_sequential_numbers.gro) has
> no
> deleted water molecules. It is the same system as solvated.gro.
>
> I believe my error is within the keepbyz.pl file, because when I input the
> command:
>
> chmod +x keepbyz.pl new_waters.gro > keep_these_waters.gro
>
> the file "keep_these_waters.gro" is an empty file.
>
> Here is my script for keepbyz.pl:
>
> #!/bin/bash
> # give new_waters.gro as first command line arguement
> upperz=5.821
> lowerz=0.574
> sol=SOL
> count=0
> cat $1 | grep "$sol" | while read line; do
> for first in $line; do
> break
> done
> if [ "$count" = 3 ]; then
> count=0
> fi
> count=$(expr $count + 1)
> if [ "$count" != 1 ]; then
> continue
> fi
> l=${#line}
> m=$(expr $l - 24) // would use -48 if velocities are also in .gro and
> -24 otherwise
> i=1
> for word in ${line:$m}; do
> if [ "$i" = 1 ]; then
> popex=$word
> else
> if [ "$i" = 2 ]; then
> popey=$word
> else
> if [ "$i" = 3 ]; then
> popez=$word
> break
> fi
> fi
> fi
> i=$(expr $i + 1)
> done
> nolx=`echo "$popez > $upperz" | bc`
> nohx=`echo "$popez < $lowerz" | bc`
> myno=$(expr $nolx + $nohx)
> if [ "$myno" != 0 ]; then
> z=${#first}
> if [ "$z" != 8 ]; then
> sfirst="[[:space:]]$first"
> else
> sfirst=$first
> fi
> `echo grep $sfirst $1`
> fi
> done
>
> I will appreciate the help!
>
> Regards,
>
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Resident Assistant, Castor Hall Engineering Living Learning Community
> 2016-2017
> Undergraduate Researcher, Global Center for Hearing and Speech Research
> Honors College Engineering Peer Advisor
> <https://www.linkedin.com/pub/sanim-rahman/108/a64/986>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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[gmx-users] Removal of Waters in Hydrophobic Core
Hello,
I am currently working through the second tutorial of the Bevan Labs KALP15
simulation. I am attempting to use the keepbyz.pl script to remove the
waters in the hydrophobic core. I have designated a upperz and
lowerz coordinated and followed the entire section highlighted in the
instructions, however, my output (new_system_sequential_numbers.gro) has no
deleted water molecules. It is the same system as solvated.gro.
I believe my error is within the keepbyz.pl file, because when I input the
command:
chmod +x keepbyz.pl new_waters.gro > keep_these_waters.gro
the file "keep_these_waters.gro" is an empty file.
Here is my script for keepbyz.pl:
#!/bin/bash
# give new_waters.gro as first command line arguement
upperz=5.821
lowerz=0.574
sol=SOL
count=0
cat $1 | grep "$sol" | while read line; do
for first in $line; do
break
done
if [ "$count" = 3 ]; then
count=0
fi
count=$(expr $count + 1)
if [ "$count" != 1 ]; then
continue
fi
l=${#line}
m=$(expr $l - 24) // would use -48 if velocities are also in .gro and
-24 otherwise
i=1
for word in ${line:$m}; do
if [ "$i" = 1 ]; then
popex=$word
else
if [ "$i" = 2 ]; then
popey=$word
else
if [ "$i" = 3 ]; then
popez=$word
break
fi
fi
fi
i=$(expr $i + 1)
done
nolx=`echo "$popez > $upperz" | bc`
nohx=`echo "$popez < $lowerz" | bc`
myno=$(expr $nolx + $nohx)
if [ "$myno" != 0 ]; then
z=${#first}
if [ "$z" != 8 ]; then
sfirst="[[:space:]]$first"
else
sfirst=$first
fi
`echo grep $sfirst $1`
fi
done
I will appreciate the help!
Regards,
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Undergraduate Researcher, Global Center for Hearing and Speech Research
Honors College Engineering Peer Advisor
<https://www.linkedin.com/pub/sanim-rahman/108/a64/986>
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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* For (un)subscribe requests visit
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[gmx-users] Post Permission
Hello, I would like access to post to the mailing list. Thank you! Regards, *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017 Undergraduate Researcher, Global Center for Hearing and Speech Research Honors College Engineering Peer Advisor <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> -- 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.
