Re: [gmx-users] tutorial problem
Hi,
Your working directory is the one in which you are doing your work. You are
making a copy of the normal force field folder, so that next time you use
it, you know it is unchanged from what GROMACS provides. Having made the
copy, edit the files in the copy.
Mark
On Sun, Jul 22, 2018, 09:49 工业131 焦凤轩 <18792742...@163.com> wrote:
> dear all
>I am a new user,I was doing this tutorial(
> http://www.mdtutorials.com/gmx/membrane_protein/index.html) it said {To
> use the parameters in lipid.itp, we will have to make some changes to our
> pre-packaged GROMOS96 53A6 force field files (in $GMXLIB/gromos53a6.ff).
> Make a copy of this directory in your working directory called
> "gromos53a6_lipid.ff"},I install gromacs in usr/local/ . ,so this WORKING
> DIRECTORY means in which layer of folder ?is it /usr/local/gromacs/
> share/gromacs/top/ ?then this tutorial said (modify forcefield.doc to
> update the description of the force field parameters in it)，so I should
> modify the forcefield .doc in the new created folder called
> gromos53a6_lipid.ff or the initial folder gromos53a6.ff? I will appreciate
> it if anyone can solve my problem.
>
>
> thank you
> --
> 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] tutorial problem
dear all
I am a new user,I was doing this
tutorial(http://www.mdtutorials.com/gmx/membrane_protein/index.html) it said
{To use the parameters in lipid.itp, we will have to make some changes to our
pre-packaged GROMOS96 53A6 force field files (in $GMXLIB/gromos53a6.ff). Make a
copy of this directory in your working directory called
"gromos53a6_lipid.ff"},I install gromacs in usr/local/ . ,so this WORKING
DIRECTORY means in which layer of folder ?is it /usr/local/gromacs/
share/gromacs/top/ ?then this tutorial said (modify forcefield.doc to update
the description of the force field parameters in it)，so I should modify the
forcefield .doc in the new created folder called gromos53a6_lipid.ff or the
initial folder gromos53a6.ff? I will appreciate it if anyone can solve my
problem.
thank you
--
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] Tutorial for calculating diffusion from umbrella sampling
Dear Experts,Is there any tutorial available online for understanding procedure to calculate diffusion coefficient from umbrella sampled force and position trajectory data. The formula for diffusion is given as D()=variance(z)/tau. Numerator is variance of z (or reaction coordinate) and denominator is the characteristic time. Reference for the equation is “Gerhard Hummer 2005 New J. Phys. 7 34”As a novice in MD, it’s very difficult to understand the Gerhard paper. Dow anybody have any idea about how to implement this equation.ThanksYogiSent using Zoho Mail -- 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] Tutorial
Hi, is there a tutorial for importing fully charged non-peptid topologies for the AMBER FF ISBN type to GMX somewhere ? Thanks Sergio Manzetti Fjordforsk AS Midtun 6894 VangsnesNorge Org.nr. 911 659 654 Tlf: +47 57695621Økolab | Nanofactory | AQ-Lab | FAP -- 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] Tutorial #3 : Umbrella Sampling (By Justin Lemkul)
On 6/21/16 1:49 AM, amitbe...@chemeng.iisc.ernet.in wrote: Hello, The summary_distances.dat file contains only one column ( the column for COM is missing). I am using GROMACS 5.1.2. How to solve this issue. I feel like I've answered this same exact question several times in the last week. Your invocation of gmx distance failed for some reason. Don't use the script. Run one instance of gmx distance manually and look at the error it returns. Then fix that error. -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.
[gmx-users] Tutorial #3 : Umbrella Sampling (By Justin Lemkul)
Hello, The summary_distances.dat file contains only one column ( the column for COM is missing). I am using GROMACS 5.1.2. How to solve this issue. Regards, Amit Behera Research Scholar, Dept. of Chemical Engineering, IISc -- 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] Tutorial 2: KALP-15 in DPPC
On 6/20/16 4:08 PM, Kyle Titus-Glover wrote: Sure, I can gather up the files and send them in a compressed folder to you school email if that's ok. Yes. The sequence of commands (in an executable script) is also essential. A dump of files is only a small part of the equation. -Justin Kyle Titus-Glover On Mon, Jun 20, 2016 at 3:45 PM, Justin Lemkul wrote: On 6/20/16 3:11 PM, Kyle Titus-Glover wrote: However, I did look into system_shrink1.gro and saw that the file was missing the peptides and that 2 DPPC molecules still remained undeleted. Should I manually correct the coordinate file? No, you should correct whatever it is that you're doing :) InflateGRO can't un-delete lipids and it doesn't delete protein. So you're issuing a command incorrectly, mismanaging files, or something else. As this is not actually a GROMACS problem, we can continue this off-list if needed. I will need any relevant input and output files and an exact (copy-paste) of any commands used. The tutorial works "out of the box," so there's something being mishandled if it's not. -Justin On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover wrote: I tried restarting the whole process to go back and carefully look and make sure that nothing was spelled right. Bu I still get the same error. On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul wrote: On 6/20/16 2:32 PM, Kyle Titus-Glover wrote: Hey everyone, I've been working on the Justin Lemkul's 2nd tutorial and just can't seem to get past 2. packing the lipids around the protein and 3. solvating with water. The follow the instructions step by step but for some reason as I try to run EM with gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp I get hit with this error: Fatal error: number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6438) 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 = 6400) so something has gone badly wrong here. Your coordinate file at this point should have the peptide and 126 lipids; the InflateGRO output below looks correct. Check the contents of system_shrink1.gro and make sure you haven't perhaps accidentally renamed a file something that it shouldn't be. -Justin I figured that since my number of molecules were off that the problem was either the way I updated the molecules section of my topol.top fill by adding DPPC 126 after seeing this when adding lipids: There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking for overlap ...this might actually take a while 100 % done... There are 2 lipids within cut-off range... 1 will be removed from the upper leaflet... 1 will be removed from the lower leaflet... But for some reason I can't seem to start the EM iterations because of this error. Sincerely, Kyle Titus-Glover Virginia Tech '17 | Engineering Science & Mechanics Dean's Research Assistant, College of Engineering 443-802-4058 -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == 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.
Re: [gmx-users] Tutorial 2: KALP-15 in DPPC
Sure, I can gather up the files and send them in a compressed folder to you school email if that's ok. Kyle Titus-Glover On Mon, Jun 20, 2016 at 3:45 PM, Justin Lemkul wrote: > > > On 6/20/16 3:11 PM, Kyle Titus-Glover wrote: > >> However, I did look into system_shrink1.gro and saw that the file was >> missing the peptides and that 2 DPPC molecules still remained undeleted. >> Should I manually correct the coordinate file? >> >> > No, you should correct whatever it is that you're doing :) InflateGRO > can't un-delete lipids and it doesn't delete protein. So you're issuing a > command incorrectly, mismanaging files, or something else. > > As this is not actually a GROMACS problem, we can continue this off-list > if needed. I will need any relevant input and output files and an exact > (copy-paste) of any commands used. The tutorial works "out of the box," so > there's something being mishandled if it's not. > > -Justin > > > On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover wrote: >> >> I tried restarting the whole process to go back and carefully look and >>> make sure that nothing was spelled right. Bu I still get the same error. >>> >>> >>> On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul wrote: >>> >>> On 6/20/16 2:32 PM, Kyle Titus-Glover wrote: Hey everyone, > > I've been working on the Justin Lemkul's 2nd tutorial and just can't > seem > to get past 2. packing the lipids around the protein and 3. solvating > with > water. The follow the instructions step by step but for some reason as > I > try to run EM with > > gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp > > I get hit with this error: > > Fatal error: > number of coordinates in coordinate file (system_shrink1.gro, 6400) > does not match topology (topol.top, 6438) > > > 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 = 6400) so something has gone badly wrong here. Your coordinate file at this point should have the peptide and 126 lipids; the InflateGRO output below looks correct. Check the contents of system_shrink1.gro and make sure you haven't perhaps accidentally renamed a file something that it shouldn't be. -Justin I figured that since my number of molecules were off that the problem was > either the way I updated the molecules section of my topol.top fill by > adding > DPPC 126 > > after seeing this when adding lipids: > > There are 128 lipids... > with 50 atoms per lipid.. > > Determining upper and lower leaflet... > 64 lipids in the upper... > 64 lipids in the lower leaflet > > Centering protein > Checking for overlap > ...this might actually take a while > 100 % done... > There are 2 lipids within cut-off range... > 1 will be removed from the upper leaflet... > 1 will be removed from the lower leaflet... > > But for some reason I can't seem to start the EM iterations because of > this > error. > > Sincerely, > > Kyle Titus-Glover > Virginia Tech '17 | Engineering Science & Mechanics > Dean's Research Assistant, College of Engineering > 443-802-4058 > > > -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (
Re: [gmx-users] Tutorial 2: KALP-15 in DPPC
On 6/20/16 3:11 PM, Kyle Titus-Glover wrote: However, I did look into system_shrink1.gro and saw that the file was missing the peptides and that 2 DPPC molecules still remained undeleted. Should I manually correct the coordinate file? No, you should correct whatever it is that you're doing :) InflateGRO can't un-delete lipids and it doesn't delete protein. So you're issuing a command incorrectly, mismanaging files, or something else. As this is not actually a GROMACS problem, we can continue this off-list if needed. I will need any relevant input and output files and an exact (copy-paste) of any commands used. The tutorial works "out of the box," so there's something being mishandled if it's not. -Justin On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover wrote: I tried restarting the whole process to go back and carefully look and make sure that nothing was spelled right. Bu I still get the same error. On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul wrote: On 6/20/16 2:32 PM, Kyle Titus-Glover wrote: Hey everyone, I've been working on the Justin Lemkul's 2nd tutorial and just can't seem to get past 2. packing the lipids around the protein and 3. solvating with water. The follow the instructions step by step but for some reason as I try to run EM with gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp I get hit with this error: Fatal error: number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6438) 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 = 6400) so something has gone badly wrong here. Your coordinate file at this point should have the peptide and 126 lipids; the InflateGRO output below looks correct. Check the contents of system_shrink1.gro and make sure you haven't perhaps accidentally renamed a file something that it shouldn't be. -Justin I figured that since my number of molecules were off that the problem was either the way I updated the molecules section of my topol.top fill by adding DPPC 126 after seeing this when adding lipids: There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking for overlap ...this might actually take a while 100 % done... There are 2 lipids within cut-off range... 1 will be removed from the upper leaflet... 1 will be removed from the lower leaflet... But for some reason I can't seem to start the EM iterations because of this error. Sincerely, Kyle Titus-Glover Virginia Tech '17 | Engineering Science & Mechanics Dean's Research Assistant, College of Engineering 443-802-4058 -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Tutorial 2: KALP-15 in DPPC
However, I did look into system_shrink1.gro and saw that the file was missing the peptides and that 2 DPPC molecules still remained undeleted. Should I manually correct the coordinate file? On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover wrote: > I tried restarting the whole process to go back and carefully look and > make sure that nothing was spelled right. Bu I still get the same error. > > > On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul wrote: > >> >> >> On 6/20/16 2:32 PM, Kyle Titus-Glover wrote: >> >>> Hey everyone, >>> >>> I've been working on the Justin Lemkul's 2nd tutorial and just can't seem >>> to get past 2. packing the lipids around the protein and 3. solvating >>> with >>> water. The follow the instructions step by step but for some reason as I >>> try to run EM with >>> >>> gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp >>> >>> I get hit with this error: >>> >>> Fatal error: >>> number of coordinates in coordinate file (system_shrink1.gro, 6400) >>> does not match topology (topol.top, 6438) >>> >>> >> 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 = >> 6400) so something has gone badly wrong here. Your coordinate file at this >> point should have the peptide and 126 lipids; the InflateGRO output below >> looks correct. Check the contents of system_shrink1.gro and make sure you >> haven't perhaps accidentally renamed a file something that it shouldn't be. >> >> -Justin >> >> I figured that since my number of molecules were off that the problem was >>> either the way I updated the molecules section of my topol.top fill by >>> adding >>> DPPC 126 >>> >>> after seeing this when adding lipids: >>> >>> There are 128 lipids... >>> with 50 atoms per lipid.. >>> >>> Determining upper and lower leaflet... >>> 64 lipids in the upper... >>> 64 lipids in the lower leaflet >>> >>> Centering protein >>> Checking for overlap >>> ...this might actually take a while >>> 100 % done... >>> There are 2 lipids within cut-off range... >>> 1 will be removed from the upper leaflet... >>> 1 will be removed from the lower leaflet... >>> >>> But for some reason I can't seem to start the EM iterations because of >>> this >>> error. >>> >>> Sincerely, >>> >>> Kyle Titus-Glover >>> Virginia Tech '17 | Engineering Science & Mechanics >>> Dean's Research Assistant, College of Engineering >>> 443-802-4058 >>> >>> >> -- >> == >> >> 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] Tutorial 2: KALP-15 in DPPC
I tried restarting the whole process to go back and carefully look and make sure that nothing was spelled right. Bu I still get the same error. On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul wrote: > > > On 6/20/16 2:32 PM, Kyle Titus-Glover wrote: > >> Hey everyone, >> >> I've been working on the Justin Lemkul's 2nd tutorial and just can't seem >> to get past 2. packing the lipids around the protein and 3. solvating with >> water. The follow the instructions step by step but for some reason as I >> try to run EM with >> >> gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp >> >> I get hit with this error: >> >> Fatal error: >> number of coordinates in coordinate file (system_shrink1.gro, 6400) >> does not match topology (topol.top, 6438) >> >> > 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 = > 6400) so something has gone badly wrong here. Your coordinate file at this > point should have the peptide and 126 lipids; the InflateGRO output below > looks correct. Check the contents of system_shrink1.gro and make sure you > haven't perhaps accidentally renamed a file something that it shouldn't be. > > -Justin > > I figured that since my number of molecules were off that the problem was >> either the way I updated the molecules section of my topol.top fill by >> adding >> DPPC 126 >> >> after seeing this when adding lipids: >> >> There are 128 lipids... >> with 50 atoms per lipid.. >> >> Determining upper and lower leaflet... >> 64 lipids in the upper... >> 64 lipids in the lower leaflet >> >> Centering protein >> Checking for overlap >> ...this might actually take a while >> 100 % done... >> There are 2 lipids within cut-off range... >> 1 will be removed from the upper leaflet... >> 1 will be removed from the lower leaflet... >> >> But for some reason I can't seem to start the EM iterations because of >> this >> error. >> >> Sincerely, >> >> Kyle Titus-Glover >> Virginia Tech '17 | Engineering Science & Mechanics >> Dean's Research Assistant, College of Engineering >> 443-802-4058 >> >> > -- > == > > 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] Tutorial 2: KALP-15 in DPPC
On 6/20/16 2:32 PM, Kyle Titus-Glover wrote: Hey everyone, I've been working on the Justin Lemkul's 2nd tutorial and just can't seem to get past 2. packing the lipids around the protein and 3. solvating with water. The follow the instructions step by step but for some reason as I try to run EM with gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp I get hit with this error: Fatal error: number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6438) 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 = 6400) so something has gone badly wrong here. Your coordinate file at this point should have the peptide and 126 lipids; the InflateGRO output below looks correct. Check the contents of system_shrink1.gro and make sure you haven't perhaps accidentally renamed a file something that it shouldn't be. -Justin I figured that since my number of molecules were off that the problem was either the way I updated the molecules section of my topol.top fill by adding DPPC 126 after seeing this when adding lipids: There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking for overlap ...this might actually take a while 100 % done... There are 2 lipids within cut-off range... 1 will be removed from the upper leaflet... 1 will be removed from the lower leaflet... But for some reason I can't seem to start the EM iterations because of this error. Sincerely, Kyle Titus-Glover Virginia Tech '17 | Engineering Science & Mechanics Dean's Research Assistant, College of Engineering 443-802-4058 -- == 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.
[gmx-users] Tutorial 2: KALP-15 in DPPC
Hey everyone, I've been working on the Justin Lemkul's 2nd tutorial and just can't seem to get past 2. packing the lipids around the protein and 3. solvating with water. The follow the instructions step by step but for some reason as I try to run EM with gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp I get hit with this error: Fatal error: number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6438) I figured that since my number of molecules were off that the problem was either the way I updated the molecules section of my topol.top fill by adding DPPC 126 after seeing this when adding lipids: There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking for overlap ...this might actually take a while 100 % done... There are 2 lipids within cut-off range... 1 will be removed from the upper leaflet... 1 will be removed from the lower leaflet... But for some reason I can't seem to start the EM iterations because of this error. Sincerely, Kyle Titus-Glover Virginia Tech '17 | Engineering Science & Mechanics Dean's Research Assistant, College of Engineering 443-802-4058 -- 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] Tutorial 2: KALP-15 in DPPC
Hey everyone, I've been working on the Justin Lemkul's 2nd tutorial and just can't seem to get past 2. packing the lipids around the protein and 3. solvating with water. The follow the instructions step by step but for some reason as I try to run EM with gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp I get hit with this error: Fatal error: number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6438) I figured that since my number of molecules were off that the problem was either the way I updated the molecules section of my topol.top fill by adding DPPC 126 after seeing this when adding lipids: There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking for overlap ...this might actually take a while 100 % done... There are 2 lipids within cut-off range... 1 will be removed from the upper leaflet... 1 will be removed from the lower leaflet... But for some reason I can't seem to start the EM iterations because of this error. Sincerely, Kyle Titus-Glover Virginia Tech '17 | Engineering Science & Mechanics Dean's Research Assistant, College of Engineering 443-802-4058 -- 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] tutorial for "dual" alchemical transformation in gromacs?
You still have couple-moltype set. On Tue, 1 Dec 2015 15:39:40 +0100 Sebastian Stolzenberg wrote: > OK, thanks a lot, Hannes, > > I combined the "CL-" and "NA+" into one "NC" [moleculetype] and > switched off the couple-* switches as you suggested (attached), > but I am still receiving the same warning message: > "The lambda=0 and lambda=1 states for coupling are identical" > > I guess I am almost there, am I missing something else? > > Thanks again, > Sebastian > > > > On 01.12.2015 14:22, Hannes Loeffler wrote: > > Ok, my attachment seems to have been stripped, so inline only. Hope > > it's not too bad. > > > > [ atomtypes ] > > ;name bond_type mass charge ptype sigma > > epsilon Amb > > DU DU 0.0 0.0 A 0.0e+00 > > 0.0e+00 ; 0.00 0. > > OW OW 0.0 0.0 A 3.15075e-01 > > 6.35968e-01 ; 1.77 0.1520 > > HW HW 0.0 0.0 A 0.0e+00 > > 0.0e+00 ; 0.00 0. > > > > [ moleculetype ] > > ; molname nrexcl > > NA+CL- 1 > > > > [ atoms ] > > ; DU->IP > > ; IM->DU > > ; = IM->IP > > ; id_at type res nr residu name at name cg nr charge > > mass typeB chargeB massB > > 1 DU 1NA+ NA+ 1 0 22.9898 > > IP 0 22.9898 > > 2 IM 1 DU DU2 0 35.4530 > > DU 0 35.4530 > > > > > > > > On Tue, 1 Dec 2015 13:17:38 + > > Hannes Loeffler wrote: > > > >> Dear Sebastian, > >> > >> I have got your attachment. I do not know all intricacies of > >> Gromacs but for relative free energies you only use one > >> moleculetype for the perturbed group, see attachment. You do not > >> use the couple-* switches for relative simulations. > >> > >> Yes, you are right about typeA and typeB. If you have larger > >> molecules you would just combine both molecules in their entirety > >> into one "pseudo" molecules. One original molecules has the normal > >> force field types in the A state and dummy atoms in the final, > >> while the other molecule has this reversed. > >> > >> > >> Cheers, > >> Hannes. > >> > >> > >> > >> On Tue, 1 Dec 2015 13:34:12 +0100 > >> Sebastian Stolzenberg wrote: > >> > >>> Dear Hannes, > >>> > >>>> I have some trouble reading your top file in my web browser > >>> Apologies, am not sure if this works in this list, but I am now > >>> also attaching my topol.top and grompp.mdp files. > >>> I hope this let's you see better what I am doing wrong. > >>> > >>>> As your two dummy types appear to be identical > >>>> you can define just one. > >>> Thank you, as you can see in topol.top, I now have only one dummy > >>> atom type called "XX". > >>> > >>>> I think your transformations are IPX->Na+, IMX->Cl-. > >>> my "typeA" columns are "XX" and "IM" (NA+) > >>> my "typeB" columns are "IM" and "XX" (CL-) > >>> If I understand correctly (do I?), lambda=0 corresponds to > >>> "typeA", whereas lambda=1 corresponds to "typeB", so my > >>> transformation is "XX" -> "Na+", "Cl-" -> "XX" > >>> > >>> Thanks a bunch, > >>> Sebastian > >>> > >>> > >>> > >>> On 30.11.2015 17:30, hannes.loeff...@stfc.ac.uk wrote: > >>>> Dear Sebastian, > >>>> > >>>> I have some trouble reading your top file in my web browser but I > >>>> think your transformations are IPX->Na+, IMX->Cl-. So you would > >>>> have to reverse the columns for the first atom. As your two > >>>> dummy types appear to be identical you can define just one. > >>>> > >>>> Cheers, > >>>> Hannes. > >>>> > >>>> > >>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > >>>> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of > >>>> Sebastian Stolzenberg [s.stolzenb...@fu-berlin.de] Sent:
Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?
OK, thanks a lot, Hannes, I combined the "CL-" and "NA+" into one "NC" [moleculetype] and switched off the couple-* switches as you suggested (attached), but I am still receiving the same warning message: "The lambda=0 and lambda=1 states for coupling are identical" I guess I am almost there, am I missing something else? Thanks again, Sebastian On 01.12.2015 14:22, Hannes Loeffler wrote: > Ok, my attachment seems to have been stripped, so inline only. Hope > it's not too bad. > > [ atomtypes ] > ;name bond_type mass charge ptype sigma > epsilon Amb > DU DU 0.0 0.0 A 0.0e+00 0.0e+00 ; > 0.00 0. > OW OW 0.0 0.0 A 3.15075e-01 6.35968e-01 ; > 1.77 0.1520 > HW HW 0.0 0.0 A 0.0e+00 0.0e+00 ; > 0.00 0. > > [ moleculetype ] > ; molname nrexcl > NA+CL- 1 > > [ atoms ] > ; DU->IP > ; IM->DU > ; = IM->IP > ; id_at type res nr residu name at name cg nr charge > mass typeB chargeB massB > 1 DU 1NA+ NA+ 1 0 22.9898 > IP 0 22.9898 > 2 IM 1 DU DU2 0 35.4530 > DU 0 35.4530 > > > > On Tue, 1 Dec 2015 13:17:38 + > Hannes Loeffler wrote: > >> Dear Sebastian, >> >> I have got your attachment. I do not know all intricacies of Gromacs >> but for relative free energies you only use one moleculetype for the >> perturbed group, see attachment. You do not use the couple-* switches >> for relative simulations. >> >> Yes, you are right about typeA and typeB. If you have larger >> molecules you would just combine both molecules in their entirety >> into one "pseudo" molecules. One original molecules has the normal >> force field types in the A state and dummy atoms in the final, while >> the other molecule has this reversed. >> >> >> Cheers, >> Hannes. >> >> >> >> On Tue, 1 Dec 2015 13:34:12 +0100 >> Sebastian Stolzenberg wrote: >> >>> Dear Hannes, >>> >>>> I have some trouble reading your top file in my web browser >>> Apologies, am not sure if this works in this list, but I am now also >>> attaching my topol.top and grompp.mdp files. >>> I hope this let's you see better what I am doing wrong. >>> >>>> As your two dummy types appear to be identical >>>> you can define just one. >>> Thank you, as you can see in topol.top, I now have only one dummy >>> atom type called "XX". >>> >>>> I think your transformations are IPX->Na+, IMX->Cl-. >>> my "typeA" columns are "XX" and "IM" (NA+) >>> my "typeB" columns are "IM" and "XX" (CL-) >>> If I understand correctly (do I?), lambda=0 corresponds to "typeA", >>> whereas lambda=1 corresponds to "typeB", so my transformation is >>> "XX" -> "Na+", "Cl-" -> "XX" >>> >>> Thanks a bunch, >>> Sebastian >>> >>> >>> >>> On 30.11.2015 17:30, hannes.loeff...@stfc.ac.uk wrote: >>>> Dear Sebastian, >>>> >>>> I have some trouble reading your top file in my web browser but I >>>> think your transformations are IPX->Na+, IMX->Cl-. So you would >>>> have to reverse the columns for the first atom. As your two dummy >>>> types appear to be identical you can define just one. >>>> >>>> Cheers, >>>> Hannes. >>>> >>>> >>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >>>> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of >>>> Sebastian Stolzenberg [s.stolzenb...@fu-berlin.de] Sent: 30 >>>> November 2015 16:19 To: gromacs.org_gmx-users@maillist.sys.kth.se >>>> Subject: Re: [gmx-users] tutorial for "dual" alchemical >>>> transformation in gromacs? >>>> >>>> Dear Hannes, >>>> >>>> Thank you very much for your answer. >>>> >>>>> Practical question: why would you want to do that? >>>>> Your two molecules will drift apart unless parts of the molecules >>>>> are linked together in a "single" topology fashion or or you >>>>> introduce other restrain
Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?
Ok, my attachment seems to have been stripped, so inline only. Hope it's not too bad. [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb DU DU 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OW OW 0.0 0.0 A 3.15075e-01 6.35968e-01 ; 1.77 0.1520 HW HW 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. [ moleculetype ] ; molname nrexcl NA+CL- 1 [ atoms ] ; DU->IP ; IM->DU ; = IM->IP ; id_at type res nr residu name at name cg nr charge mass typeB chargeB massB 1 DU 1NA+ NA+ 1 0 22.9898 IP 0 22.9898 2 IM 1 DU DU2 0 35.4530 DU 0 35.4530 On Tue, 1 Dec 2015 13:17:38 + Hannes Loeffler wrote: > Dear Sebastian, > > I have got your attachment. I do not know all intricacies of Gromacs > but for relative free energies you only use one moleculetype for the > perturbed group, see attachment. You do not use the couple-* switches > for relative simulations. > > Yes, you are right about typeA and typeB. If you have larger > molecules you would just combine both molecules in their entirety > into one "pseudo" molecules. One original molecules has the normal > force field types in the A state and dummy atoms in the final, while > the other molecule has this reversed. > > > Cheers, > Hannes. > > > > On Tue, 1 Dec 2015 13:34:12 +0100 > Sebastian Stolzenberg wrote: > > > Dear Hannes, > > > > > I have some trouble reading your top file in my web browser > > Apologies, am not sure if this works in this list, but I am now also > > attaching my topol.top and grompp.mdp files. > > I hope this let's you see better what I am doing wrong. > > > > > As your two dummy types appear to be identical > > > you can define just one. > > Thank you, as you can see in topol.top, I now have only one dummy > > atom type called "XX". > > > > > I think your transformations are IPX->Na+, IMX->Cl-. > > my "typeA" columns are "XX" and "IM" (NA+) > > my "typeB" columns are "IM" and "XX" (CL-) > > If I understand correctly (do I?), lambda=0 corresponds to "typeA", > > whereas lambda=1 corresponds to "typeB", so my transformation is > > "XX" -> "Na+", "Cl-" -> "XX" > > > > Thanks a bunch, > > Sebastian > > > > > > > > On 30.11.2015 17:30, hannes.loeff...@stfc.ac.uk wrote: > > > Dear Sebastian, > > > > > > I have some trouble reading your top file in my web browser but I > > > think your transformations are IPX->Na+, IMX->Cl-. So you would > > > have to reverse the columns for the first atom. As your two dummy > > > types appear to be identical you can define just one. > > > > > > Cheers, > > > Hannes. > > > > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of > > > Sebastian Stolzenberg [s.stolzenb...@fu-berlin.de] Sent: 30 > > > November 2015 16:19 To: gromacs.org_gmx-users@maillist.sys.kth.se > > > Subject: Re: [gmx-users] tutorial for "dual" alchemical > > > transformation in gromacs? > > > > > > Dear Hannes, > > > > > > Thank you very much for your answer. > > > > > >> Practical question: why would you want to do that? > > >> Your two molecules will drift apart unless parts of the molecules > > >> are linked together in a "single" topology fashion or or you > > >> introduce other restraints/constraints. > > > I am doing some method development, so my plan is to currently fix > > > all atoms of A and B. > > > > > >> In practice, you can do that with Gromacs relatively easily. The > > >> manual describes how to set up the A and the B state of a > > >> molecule. > > > OK, thanks. As a start, I set up a simple "Cl->Na in a water box" > > > system: > > > > > > gro file: > > > 1 Na+ NA+1 1.434 1.045 1.049 > > > 2 Cl- CL-2 1.434 1.045 1.049 > > > 3 WATO3 2.914 1.241 1.997 > > > 3 WAT H14 2.899 1.335 1.984 > > > 3 WAT H25 2.8
Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?
Dear Sebastian, I have got your attachment. I do not know all intricacies of Gromacs but for relative free energies you only use one moleculetype for the perturbed group, see attachment. You do not use the couple-* switches for relative simulations. Yes, you are right about typeA and typeB. If you have larger molecules you would just combine both molecules in their entirety into one "pseudo" molecules. One original molecules has the normal force field types in the A state and dummy atoms in the final, while the other molecule has this reversed. Cheers, Hannes. On Tue, 1 Dec 2015 13:34:12 +0100 Sebastian Stolzenberg wrote: > Dear Hannes, > > > I have some trouble reading your top file in my web browser > Apologies, am not sure if this works in this list, but I am now also > attaching my topol.top and grompp.mdp files. > I hope this let's you see better what I am doing wrong. > > > As your two dummy types appear to be identical > > you can define just one. > Thank you, as you can see in topol.top, I now have only one dummy atom > type called "XX". > > > I think your transformations are IPX->Na+, IMX->Cl-. > my "typeA" columns are "XX" and "IM" (NA+) > my "typeB" columns are "IM" and "XX" (CL-) > If I understand correctly (do I?), lambda=0 corresponds to "typeA", > whereas lambda=1 corresponds to "typeB", so my transformation is > "XX" -> "Na+", "Cl-" -> "XX" > > Thanks a bunch, > Sebastian > > > > On 30.11.2015 17:30, hannes.loeff...@stfc.ac.uk wrote: > > Dear Sebastian, > > > > I have some trouble reading your top file in my web browser but I > > think your transformations are IPX->Na+, IMX->Cl-. So you would > > have to reverse the columns for the first atom. As your two dummy > > types appear to be identical you can define just one. > > > > Cheers, > > Hannes. > > > > ____________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of > > Sebastian Stolzenberg [s.stolzenb...@fu-berlin.de] Sent: 30 > > November 2015 16:19 To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] tutorial for "dual" alchemical > > transformation in gromacs? > > > > Dear Hannes, > > > > Thank you very much for your answer. > > > >> Practical question: why would you want to do that? > >> Your two molecules will drift apart unless parts of the molecules > >> are linked together in a "single" topology fashion or or you > >> introduce other restraints/constraints. > > I am doing some method development, so my plan is to currently fix > > all atoms of A and B. > > > >> In practice, you can do that with Gromacs relatively easily. The > >> manual describes how to set up the A and the B state of a molecule. > > OK, thanks. As a start, I set up a simple "Cl->Na in a water box" > > system: > > > > gro file: > > 1 Na+ NA+1 1.434 1.045 1.049 > > 2 Cl- CL-2 1.434 1.045 1.049 > > 3 WATO3 2.914 1.241 1.997 > > 3 WAT H14 2.899 1.335 1.984 > > 3 WAT H25 2.841 1.212 2.052 > > ... > > > > i.e., I transform a "Cl-" into a "Na+" by de-coupling > > (annihiliating) the non-bonded interactions of "Cl-" and coupling > > (letting appear) the ones for "Na+". This I attempt by defining > > "dummy" atom types IMX and IPX for Cl- and Na+, respectively: > > > > top file: > > ... > > [ atomtypes ] > > ;name bond_type mass charge ptype sigma > > epsilon Amb > > IP IP 0.0 0.0 A 3.32840e-01 > > 1.15897e-02 ; 1.87 0.0028 > > IM IM 0.0 0.0 A 4.40104e-01 > > 4.18400e-01 ; 2.47 0.1000 > > IPX IP 0.0 0.0 A 0.0e+00 > > 0.0e+00 ; 0.00 0. > > IMX IM 0.0 0.0 A 0.0e+00 > > 0.0e+00 ; 0.00 0. > > ... > > [ atoms ] > > ; id_at type res nr residu name at name cg nr charge > > mass typeB chargeB massB > > 1 IPX 1 NA+ NA+ 1 0 > > 22.9898 IP 0 22.9898 > > ... > > [ atoms ] > > ; id_at type res nr residu name at name cg nr charge > > mass typeB
Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?
Dear Hannes, > I have some trouble reading your top file in my web browser Apologies, am not sure if this works in this list, but I am now also attaching my topol.top and grompp.mdp files. I hope this let's you see better what I am doing wrong. > As your two dummy types appear to be identical > you can define just one. Thank you, as you can see in topol.top, I now have only one dummy atom type called "XX". > I think your transformations are IPX->Na+, IMX->Cl-. my "typeA" columns are "XX" and "IM" (NA+) my "typeB" columns are "IM" and "XX" (CL-) If I understand correctly (do I?), lambda=0 corresponds to "typeA", whereas lambda=1 corresponds to "typeB", so my transformation is "XX" -> "Na+", "Cl-" -> "XX" Thanks a bunch, Sebastian On 30.11.2015 17:30, hannes.loeff...@stfc.ac.uk wrote: > Dear Sebastian, > > I have some trouble reading your top file in my web browser but I think your > transformations are IPX->Na+, IMX->Cl-. So you would have to reverse the > columns for the first atom. As your two dummy types appear to be identical > you can define just one. > > Cheers, > Hannes. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian > Stolzenberg [s.stolzenb...@fu-berlin.de] > Sent: 30 November 2015 16:19 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] tutorial for "dual" alchemical transformation in > gromacs? > > Dear Hannes, > > Thank you very much for your answer. > >> Practical question: why would you want to do that? >> Your two molecules will drift apart unless parts of the molecules are >> linked together in a "single" topology fashion or or you introduce >> other restraints/constraints. > I am doing some method development, so my plan is to currently fix all > atoms of A and B. > >> In practice, you can do that with Gromacs relatively easily. The >> manual describes how to set up the A and the B state of a molecule. > OK, thanks. As a start, I set up a simple "Cl->Na in a water box" system: > > gro file: > 1 Na+ NA+1 1.434 1.045 1.049 > 2 Cl- CL-2 1.434 1.045 1.049 > 3 WATO3 2.914 1.241 1.997 > 3 WAT H14 2.899 1.335 1.984 > 3 WAT H25 2.841 1.212 2.052 > ... > > i.e., I transform a "Cl-" into a "Na+" by de-coupling (annihiliating) > the non-bonded interactions of "Cl-" and coupling (letting appear) the > ones for "Na+". This I attempt by defining "dummy" atom types IMX and > IPX for Cl- and Na+, respectively: > > top file: > ... > [ atomtypes ] > ;name bond_type mass charge ptype sigma epsilon > Amb > IP IP 0.0 0.0 A 3.32840e-01 1.15897e-02 > ; 1.87 0.0028 > IM IM 0.0 0.0 A 4.40104e-01 4.18400e-01 > ; 2.47 0.1000 > IPX IP 0.0 0.0 A 0.0e+00 0.0e+00 > ; 0.00 0. > IMX IM 0.0 0.0 A 0.0e+00 0.0e+00 > ; 0.00 0. > ... > [ atoms ] > ; id_at type res nr residu name at name cg nr charge mass > typeB chargeB massB > 1 IPX 1 NA+ NA+ 1 0 > 22.9898 IP 0 22.9898 > ... > [ atoms ] > ; id_at type res nr residu name at name cg nr charge mass > typeB chargeB massB > 1 IM 1 CL- CL- 1 0 > 35.45300 IMX0 35.45300 > > (Please note that for now, I artificially set the charge of each ion to > zero to avoid total charge differences for different lambda values. > Also, for "Cl->Na", this strategy is certainly more complicated, but in > principle allows for different numbers of atoms between molecule A and B > in the "A->B" transformation.) > Unfortunately, running grompp with the standard run.mdp file from > http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf > (I omitted "couple-lambda0" and "couple-lambda1" > and set "couple-moltype = NA+ CL-") > I am puzzled by the following error message: > "The lambda=0 and lambda=1 states for coupling are identical" > > Is it possible from this error message to see what I am doing wrong? > > Many Thanks, > Sebastian > > > > > On 29.11.2015 14:36, hannes.loeff...@stfc.ac.uk wrot
Re: [gmx-users] tutorial umbrella sampling
Thanks, that did the trick! Now everything works fine. Am 29.11.2015 um 12:00 schrieb gromacs.org_gmx-users-requ...@maillist.sys.kth.se: On 11/27/15 5:36 PM, Matthias Kiesel wrote: Hi All, I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have a problem with creating the right configurations for the umbrella sampling run. After running the first pull simulation and the given perl script the com distances don?t go from 0.5nm to 5nm, instead they start at 0nm, go negative for a some time grow until ~0.3nm and go back to small and negative values again.? That's definitely not right. Visualize the trajectory - does this match the behavior there? The pull should be pretty straightforward. When I visualize some of the .gro files (like conf250.gro) I can see something being pulled away from the rest of the Protein (how can I verify its Chain_A?) It's the first peptide, numerically, and you created an index group for it in a prior step in the tutorial. and in the created pullx.xvg the desired a COM-Distance curve going from 0.5nm to ~5nm is shown. Thats why i thought it?s a issue with the perl script or the trjconv / distance commands so that the wrong distances are extracted from the trajectories, but i couldn?t resolve it. I used the following trjconv command and the provided provided perl script: Typo in the script. In the gmx distance command, it should be -oall instead of -oxyz. gmx trjconv -s pull.tpr -f traj_comp.xtc -o configs/conf.gro -sep // There was not traj.xtc file, only a traj_comp.xtc, any explanations? New default naming. I fixed the typo in the tutorial. It should be traj_comp.xtc. -Justin -- 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] tutorial for "dual" alchemical transformation in gromacs?
Dear Sebastian, I have some trouble reading your top file in my web browser but I think your transformations are IPX->Na+, IMX->Cl-. So you would have to reverse the columns for the first atom. As your two dummy types appear to be identical you can define just one. Cheers, Hannes. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian Stolzenberg [s.stolzenb...@fu-berlin.de] Sent: 30 November 2015 16:19 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs? Dear Hannes, Thank you very much for your answer. > Practical question: why would you want to do that? > Your two molecules will drift apart unless parts of the molecules are > linked together in a "single" topology fashion or or you introduce > other restraints/constraints. I am doing some method development, so my plan is to currently fix all atoms of A and B. > In practice, you can do that with Gromacs relatively easily. The > manual describes how to set up the A and the B state of a molecule. OK, thanks. As a start, I set up a simple "Cl->Na in a water box" system: gro file: 1 Na+ NA+1 1.434 1.045 1.049 2 Cl- CL-2 1.434 1.045 1.049 3 WATO3 2.914 1.241 1.997 3 WAT H14 2.899 1.335 1.984 3 WAT H25 2.841 1.212 2.052 ... i.e., I transform a "Cl-" into a "Na+" by de-coupling (annihiliating) the non-bonded interactions of "Cl-" and coupling (letting appear) the ones for "Na+". This I attempt by defining "dummy" atom types IMX and IPX for Cl- and Na+, respectively: top file: ... [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb IP IP 0.0 0.0 A 3.32840e-01 1.15897e-02 ; 1.87 0.0028 IM IM 0.0 0.0 A 4.40104e-01 4.18400e-01 ; 2.47 0.1000 IPX IP 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. IMX IM 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. ... [ atoms ] ; id_at type res nr residu name at name cg nr charge mass typeB chargeB massB 1 IPX 1 NA+ NA+ 1 0 22.9898 IP 0 22.9898 ... [ atoms ] ; id_at type res nr residu name at name cg nr charge mass typeB chargeB massB 1 IM 1 CL- CL- 1 0 35.45300 IMX0 35.45300 (Please note that for now, I artificially set the charge of each ion to zero to avoid total charge differences for different lambda values. Also, for "Cl->Na", this strategy is certainly more complicated, but in principle allows for different numbers of atoms between molecule A and B in the "A->B" transformation.) Unfortunately, running grompp with the standard run.mdp file from http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf (I omitted "couple-lambda0" and "couple-lambda1" and set "couple-moltype = NA+ CL-") I am puzzled by the following error message: "The lambda=0 and lambda=1 states for coupling are identical" Is it possible from this error message to see what I am doing wrong? Many Thanks, Sebastian On 29.11.2015 14:36, hannes.loeff...@stfc.ac.uk wrote: > Practical question: why would you want to do that? Your two molecules will > drift apart unless parts of the molecules are linked together in a "single" > topology fashion or or you introduce other restraints/constraints. > > In practice, you can do that with Gromacs relatively easily. The manual > describes how to set up the A and the B state of a molecule. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian > Stolzenberg [s.stolzenb...@fu-berlin.de] > Sent: 29 November 2015 13:11 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] tutorial for "dual" alchemical transformation in > gromacs? > > Dear Gromacs experts, > > I am looking for a Gromacs tutorial to perform a "dual" alchemical > transformation in a water box, i.e. a mutation or any other alchemical > transformation, in which: > the nonbonded interactions between the environment and a molecule A > disappear as lambda goes from 0 to 1, and > the nonbonded interactions between the environment and a molecule B > appears simultaneously. > Interactions between atoms A and B are to be excluded. > > So far, I have been trying to use the Gromacs user guide to extend the > et
Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?
Dear Hannes, Thank you very much for your answer. > Practical question: why would you want to do that? > Your two molecules will drift apart unless parts of the molecules are > linked together in a "single" topology fashion or or you introduce > other restraints/constraints. I am doing some method development, so my plan is to currently fix all atoms of A and B. > In practice, you can do that with Gromacs relatively easily. The > manual describes how to set up the A and the B state of a molecule. OK, thanks. As a start, I set up a simple "Cl->Na in a water box" system: gro file: 1 Na+ NA+1 1.434 1.045 1.049 2 Cl- CL-2 1.434 1.045 1.049 3 WATO3 2.914 1.241 1.997 3 WAT H14 2.899 1.335 1.984 3 WAT H25 2.841 1.212 2.052 ... i.e., I transform a "Cl-" into a "Na+" by de-coupling (annihiliating) the non-bonded interactions of "Cl-" and coupling (letting appear) the ones for "Na+". This I attempt by defining "dummy" atom types IMX and IPX for Cl- and Na+, respectively: top file: ... [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb IP IP 0.0 0.0 A 3.32840e-01 1.15897e-02 ; 1.87 0.0028 IM IM 0.0 0.0 A 4.40104e-01 4.18400e-01 ; 2.47 0.1000 IPX IP 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. IMX IM 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. ... [ atoms ] ; id_at type res nr residu name at name cg nr charge mass typeB chargeB massB 1 IPX 1 NA+ NA+ 1 0 22.9898 IP 0 22.9898 ... [ atoms ] ; id_at type res nr residu name at name cg nr charge mass typeB chargeB massB 1 IM 1 CL- CL- 1 0 35.45300 IMX0 35.45300 (Please note that for now, I artificially set the charge of each ion to zero to avoid total charge differences for different lambda values. Also, for "Cl->Na", this strategy is certainly more complicated, but in principle allows for different numbers of atoms between molecule A and B in the "A->B" transformation.) Unfortunately, running grompp with the standard run.mdp file from http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf (I omitted "couple-lambda0" and "couple-lambda1" and set "couple-moltype = NA+ CL-") I am puzzled by the following error message: "The lambda=0 and lambda=1 states for coupling are identical" Is it possible from this error message to see what I am doing wrong? Many Thanks, Sebastian On 29.11.2015 14:36, hannes.loeff...@stfc.ac.uk wrote: > Practical question: why would you want to do that? Your two molecules will > drift apart unless parts of the molecules are linked together in a "single" > topology fashion or or you introduce other restraints/constraints. > > In practice, you can do that with Gromacs relatively easily. The manual > describes how to set up the A and the B state of a molecule. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian > Stolzenberg [s.stolzenb...@fu-berlin.de] > Sent: 29 November 2015 13:11 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] tutorial for "dual" alchemical transformation in > gromacs? > > Dear Gromacs experts, > > I am looking for a Gromacs tutorial to perform a "dual" alchemical > transformation in a water box, i.e. a mutation or any other alchemical > transformation, in which: > the nonbonded interactions between the environment and a molecule A > disappear as lambda goes from 0 to 1, and > the nonbonded interactions between the environment and a molecule B > appears simultaneously. > Interactions between atoms A and B are to be excluded. > > So far, I have been trying to use the Gromacs user guide to extend the > ethanol tutorial > http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf > into such a "dual" transformation, but also because I am currently faced > with manually manipulating my topology file, this option is highly prone > to my own errors. > > Would you be able to help? > > With Thanks and Best Regards, > Sebastian > -- > 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 > ht
Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?
Practical question: why would you want to do that? Your two molecules will drift apart unless parts of the molecules are linked together in a "single" topology fashion or or you introduce other restraints/constraints. In practice, you can do that with Gromacs relatively easily. The manual describes how to set up the A and the B state of a molecule. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian Stolzenberg [s.stolzenb...@fu-berlin.de] Sent: 29 November 2015 13:11 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] tutorial for "dual" alchemical transformation in gromacs? Dear Gromacs experts, I am looking for a Gromacs tutorial to perform a "dual" alchemical transformation in a water box, i.e. a mutation or any other alchemical transformation, in which: the nonbonded interactions between the environment and a molecule A disappear as lambda goes from 0 to 1, and the nonbonded interactions between the environment and a molecule B appears simultaneously. Interactions between atoms A and B are to be excluded. So far, I have been trying to use the Gromacs user guide to extend the ethanol tutorial http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf into such a "dual" transformation, but also because I am currently faced with manually manipulating my topology file, this option is highly prone to my own errors. Would you be able to help? With Thanks and Best Regards, Sebastian -- 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] tutorial for "dual" alchemical transformation in gromacs?
Dear Gromacs experts, I am looking for a Gromacs tutorial to perform a "dual" alchemical transformation in a water box, i.e. a mutation or any other alchemical transformation, in which: the nonbonded interactions between the environment and a molecule A disappear as lambda goes from 0 to 1, and the nonbonded interactions between the environment and a molecule B appears simultaneously. Interactions between atoms A and B are to be excluded. So far, I have been trying to use the Gromacs user guide to extend the ethanol tutorial http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf into such a "dual" transformation, but also because I am currently faced with manually manipulating my topology file, this option is highly prone to my own errors. Would you be able to help? With Thanks and Best Regards, Sebastian -- 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] tutorial umbrella sampling
On 11/27/15 5:36 PM, Matthias Kiesel wrote: Hi All, I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have a problem with creating the right configurations for the umbrella sampling run. After running the first pull simulation and the given perl script the com distances don´t go from 0.5nm to 5nm, instead they start at 0nm, go negative for a some time grow until ~0.3nm and go back to small and negative values again. That's definitely not right. Visualize the trajectory - does this match the behavior there? The pull should be pretty straightforward. When I visualize some of the .gro files (like conf250.gro) I can see something being pulled away from the rest of the Protein (how can I verify its Chain_A?) It's the first peptide, numerically, and you created an index group for it in a prior step in the tutorial. and in the created pullx.xvg the desired a COM-Distance curve going from 0.5nm to ~5nm is shown. Thats why i thought it´s a issue with the perl script or the trjconv / distance commands so that the wrong distances are extracted from the trajectories, but i couldn´t resolve it. I used the following trjconv command and the provided provided perl script: Typo in the script. In the gmx distance command, it should be -oall instead of -oxyz. gmx trjconv -s pull.tpr -f traj_comp.xtc -o configs/conf.gro -sep // There was not traj.xtc file, only a traj_comp.xtc, any explanations? New default naming. I fixed the typo in the tutorial. It should be traj_comp.xtc. -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.
[gmx-users] tutorial umbrella sampling
Hi All, I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have a problem with creating the right configurations for the umbrella sampling run. After running the first pull simulation and the given perl script the com distances don´t go from 0.5nm to 5nm, instead they start at 0nm, go negative for a some time grow until ~0.3nm and go back to small and negative values again. When I visualize some of the .gro files (like conf250.gro) I can see something being pulled away from the rest of the Protein (how can I verify its Chain_A?) and in the created pullx.xvg the desired a COM-Distance curve going from 0.5nm to ~5nm is shown. Thats why i thought it´s a issue with the perl script or the trjconv / distance commands so that the wrong distances are extracted from the trajectories, but i couldn´t resolve it. I used the following trjconv command and the provided provided perl script: gmx trjconv -s pull.tpr -f traj_comp.xtc -o configs/conf.gro -sep // There was not traj.xtc file, only a traj_comp.xtc, any explanations? I did the rest of the tutorial as suggested. I hope someone is nice enough to give me a hint to a solution :) Greetings Matthias -- 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] tutorial
Hi Urszula, I suspect it's a naming inconsistency or the tutorial got garbled. Maybe you can contact Adrien Melquiond about this. Cheers, Tsjerk On Thu, Oct 15, 2015 at 1:02 PM, Urszula Uciechowska < urszula.uciechow...@biotech.ug.edu.pl> wrote: > Dear all, > > I am trying to follow the tutorial: > http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html > > Part: > ANALYSIS OF DYNAMICS AND TIME-AVERAGED PROPERTIES > > > In the command: > trjconv -f traj_helix.xtc -o traj_helix_10-50ns.xtc -n > _peptide_index.ndx -pbc nojump -dt 100 -b 1 > > > what is the traj_helix.xtc? > > Thank you in advance for your help. > > best regards > Urszula Uciechowska > > > > University of Gdansk and Medical Univesity of Gdansk > Department of Molecular and Cellular Biology > ul. Kladki 24 > 80-822 Gdansk > Poland > > > - > Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego > http://www.ug.edu.pl/ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] tutorial
Dear all, I am trying to follow the tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Part: ANALYSIS OF DYNAMICS AND TIME-AVERAGED PROPERTIES In the command: trjconv -f traj_helix.xtc -o traj_helix_10-50ns.xtc -n _peptide_index.ndx -pbc nojump -dt 100 -b 1 what is the traj_helix.xtc? Thank you in advance for your help. best regards Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] tutorial
Dear all, I am trying to follow the tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Part: ANALYSIS OF DYNAMICS AND TIME-AVERAGED PROPERTIES In the command: trjconv -f traj_helix.xtc -o traj_helix_10-50ns.xtc -n _peptide_index.ndx -pbc nojump -dt 100 -b 1 what is the traj_helix.xtc? Thank you in advance for your help. best regards Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] Tutorial site down
Thanks to the efforts of my colleagues back at Virginia Tech, we have migrated to a new server that should be more reliable than our old one, which had been showing its age for some time. The tutorial site should be back up and running. Please contact me directly if anything does not work as expected. -Justin On 6/2/15 10:12 AM, Justin Lemkul wrote: All, Yesterday we experienced a hardware failure on the server that hosts my GROMACS tutorials. We are aware of the issue and are going to be setting up a new server. The tutorials may end up on this new server or another; I haven't decided yet. For the next few days, the tutorials will be unavailable. I apologize for any inconvenience and we will get the materials back up as soon as possible. -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.
Re: [gmx-users] Tutorial site down
Dear Justin, I hope all thing will be on its road soon :) Tuong Vy 2015-06-02 23:12 GMT+09:00 Justin Lemkul : > > All, > > Yesterday we experienced a hardware failure on the server that hosts my > GROMACS tutorials. We are aware of the issue and are going to be setting > up a new server. The tutorials may end up on this new server or another; I > haven't decided yet. For the next few days, the tutorials will be > unavailable. > > I apologize for any inconvenience and we will get the materials back up as > soon as possible. > > -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] Tutorial site down
All, Yesterday we experienced a hardware failure on the server that hosts my GROMACS tutorials. We are aware of the issue and are going to be setting up a new server. The tutorials may end up on this new server or another; I haven't decided yet. For the next few days, the tutorials will be unavailable. I apologize for any inconvenience and we will get the materials back up as soon as possible. -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.
Re: [gmx-users] Tutorial For Installing Gromacs on window
On 3/19/15 12:30 AM, Rajneet kaur Saini wrote: Greetings, I want to install gromacs on window 7. but i don't know the exact procedure.could you please explain me the procedure to install gromacs on window. Thanking you in anticipation http://www.gromacs.org/Documentation/Installation_Instructions#building-on-windows -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.
[gmx-users] Tutorial For Installing Gromacs on window
Greetings, I want to install gromacs on window 7. but i don't know the exact procedure.could you please explain me the procedure to install gromacs on window. Thanking you in anticipation -- 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] Tutorial updates
On 7/9/14, 2:40 PM, Oliver Stueker wrote: Hi Justin, Do you plan to keep the Gromacs 4.x versions of your tutorials (which by the way are excellent) around for a little longer as well? From my experience It will still take quite some time until Gromacs 5 is available on most Clusters and Linux-package repositories, whereas the Gromacs 4 versions are readily available. The old tutorials are (mostly) still available. Just append "_old" to the URL for the tutorial title, e.g. "lysozyme_old" in place of just "lysozyme." A couple of the tutorials I simply converted (vsites and biphasic) because there are so few steps (they are hardly "tutorials," just demonstrations) that there was no sense in making a "backup" for the old version. Ultimately, the old versions will go away. There's already a large amount of upkeep and user feedback to take care of, and I simply don't have time to keep track of multiple versions of things. Additionally, anyone who has worked through any of the tutorials who would like to look through the new ones to make sure everything makes sense - feedback would be appreciated. I'm basically just converting command syntax and updating .mdp files, but I'm not regenerating all of the data, so if anything is going haywire, I don't know yet :) -Justin Best, Oliver On Mon, Jul 7, 2014 at 7:48 AM, Justin Lemkul wrote: All, For anyone using my tutorials, you will notice some changes in the coming days. I am updating all of them to be compatible with the newly released Gromacs version 5.0. Most of these changes will be superficial, such as small changes to command names or options. I have already updated all of the tutorials except the ones related to free energy calculations, since these will require the greatest amount of work given the changes in .mdp options. Be advised that content will be somewhat fluid over the next few days, as I find time to make the necessary changes. Feedback on clarity and correctness is always welcome. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Tutorial updates
Hi Justin, Do you plan to keep the Gromacs 4.x versions of your tutorials (which by the way are excellent) around for a little longer as well? >From my experience It will still take quite some time until Gromacs 5 is available on most Clusters and Linux-package repositories, whereas the Gromacs 4 versions are readily available. Best, Oliver On Mon, Jul 7, 2014 at 7:48 AM, Justin Lemkul wrote: > > All, > > For anyone using my tutorials, you will notice some changes in the coming > days. I am updating all of them to be compatible with the newly released > Gromacs version 5.0. Most of these changes will be superficial, such as > small changes to command names or options. I have already updated all of > the tutorials except the ones related to free energy calculations, since > these will require the greatest amount of work given the changes in .mdp > options. > > Be advised that content will be somewhat fluid over the next few days, as > I find time to make the necessary changes. Feedback on clarity and > correctness is always welcome. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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] Tutorial updates
All, For anyone using my tutorials, you will notice some changes in the coming days. I am updating all of them to be compatible with the newly released Gromacs version 5.0. Most of these changes will be superficial, such as small changes to command names or options. I have already updated all of the tutorials except the ones related to free energy calculations, since these will require the greatest amount of work given the changes in .mdp options. Be advised that content will be somewhat fluid over the next few days, as I find time to make the necessary changes. Feedback on clarity and correctness is always welcome. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] tutorial for relative free energy calculations
Dear Gromacs Users Hi. Is there a Gromacs tutorial for relative free energy calculations (solvation or binding)? Thanks in advance, Best regards, Asaf From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of lloyd riggs [lloyd.ri...@gmx.ch] Sent: Monday, December 16, 2013 1:17 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Bin files of g_sham I will attempt an answer, however there might be a better response. It depends on your input .xvg (what the first column is) and what you are telling it to do (defualt is time), and if these correspond to your time frames (can be timepoint or siply frame # I believe). g_sham seems (to me) to work like a comand line spread sheet manipulator with some built in functions. If you want a particular frame from a trajectory time point, then use g_traj with the first/last set to the frame you want but there's also 2 other tools that do this the same way... Stephan Watkins Gesendet: Sonntag, 15. Dezember 2013 um 14:49 Uhr Von: "Ankita Naithani" An: "Discussion list for GROMACS users" Betreff: [gmx-users] Bin files of g_sham Hi, I had a query regarding the bin files generated by g_sham. Does the bin index contain timepoints? i.e. there are 1024 bins so each bin has a number of time points? And supposes bin 756 has numbers like 3876, 20020, 7896 so these would all correspond to time and we could then dump the representative frame corresponding to these time points? I am a little confused as to what is stored in the bins? Timepoints or frame number and then alternatively how to get the representative frame/snapshot stored at that specific bin number. Kind regards, -- Ankita Naithani -- 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.
