Re: [gmx-users] Free volume variation during the simulation
I am simulating Crystal System (C60 molecules) Thanks, Mohamed On Wed, May 6, 2020 at 1:22 AM Arun Srikanth wrote: > Are you simulating a crystal or amorphous system? > > Arun > > On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal > wrote: > > > Hello everybody, > > > > I have two fundamental questions please. > > > > I have measured the fee volume and I discovered that, the free volume > > changes with respect to the time during the production run (different > value > > for each frame). However I have measured the density but the result does > > not change with respect to time. > > > > Shouldn't the density also changes with time if the free volume changes > > with time ? > > > > I also can't understand why the free volume changes with respect to the > > time, if the number of molecules and volume of box didn't change. > > > > Many Thanks, > > Mohamed > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free volume variation during the simulation
Are you simulating a crystal or amorphous system? Arun On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal wrote: > Hello everybody, > > I have two fundamental questions please. > > I have measured the fee volume and I discovered that, the free volume > changes with respect to the time during the production run (different value > for each frame). However I have measured the density but the result does > not change with respect to time. > > Shouldn't the density also changes with time if the free volume changes > with time ? > > I also can't understand why the free volume changes with respect to the > time, if the number of molecules and volume of box didn't change. > > Many Thanks, > Mohamed > -- > 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] Free volume variation during the simulation
Hello everybody, I have two fundamental questions please. I have measured the fee volume and I discovered that, the free volume changes with respect to the time during the production run (different value for each frame). However I have measured the density but the result does not change with respect to time. Shouldn't the density also changes with time if the free volume changes with time ? I also can't understand why the free volume changes with respect to the time, if the number of molecules and volume of box didn't change. Many Thanks, Mohamed -- 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] How to apply position restrain on selected atoms in .gro files in Gromacs?
Thank you Justin, you are a life saver..! It's working now. You have correctly pointed out the issue. Thank you so much.. :) Regards, Debashish On Wed, May 6, 2020 at 12:11 AM Justin Lemkul wrote: > > > On 5/5/20 5:54 PM, Debashish Banerjee wrote: > > Dear gmx users, > > > > I have been stuck in a problem for a month now and have scrutinized all > the > > past discussions and forms related to it dating as back as 9 years. Now I > > really need your help. > > > > My system has Clays (layered philosillacates), Cesium ions (Cs), acetate > > molecules as well as water. In total 24241 atoms in the whole system. I > > want to perform free energy calculations *(PMF)* via *umbrella sampling*. > > > > The whole idea is that I want to fix one Cs atom (atom number/index > number~ > > 5790) near to the basal surface (top layer) of clay and put in use of > the* > > pull* code as described in umbrella sampling and thereafter perform > *WHAM* > > calculations to see the progression of COM distance between (Cs) and the > > surface oxygen's present on the top layer of clay sheet over time. > > > > When, I see it in my .gro files, I can find all 16 Cs atoms ranging from > > index number (5785-5780). I just want to fix a particular single Cs atom > > (index number 5790) as mentioned above. For this I create a special index > > file which now has an extra group containing just 1 Cs atom. After this, > I > > take in the use of gmx genrestr command : > > *gmx genrestr -f npt.gro -n index.ndx -o posre_Cs.itp -fc 0 0 1000* > > This commands redirects to the newly created group from the index file > > which I created above and put constraints in it. > > > > *Step 1 * > > The *posre_Cs.itp* file looks like this: > > [ position_restraints ] > > ; ifunct fcxfcyfcz > > 5790 1 00 1000 > > > > * Step 2 * > > *My topology should include an if statement, so I also define it like > this:* > > > > #include "../charmm36.ff/forcefield.itp" > > > > ; include params for ClayFF > > #include "../ClayFF.ff/ffnonbonded.itp" > > > > ; Include topology for Clay Montmorillonite (MMT) > > #include "../ClayFF.ff/MMT_UC/UC2.itp" > > #include "../ClayFF.ff/MMT_UC/UC1.itp" > > #include "../ClayFF.ff/MMT_UC/UC3B.itp" > > #include "../ClayFF.ff/MMT_UC/UC3T.itp" > > > > ; Added the part of defining ions.itp which contains Cs atom and defined > > position restrain parameters > > > > > > > > > > *#include "../ClayFF.ff/ions.itp"#ifdef POSRES_Cs#include > > "posres_Cs.itp"#endif* > > #include "../charmm36.ff/spc.itp" > > > > #include "../charmm36.ff/organics/act.itp" > > > > [ system ] > > ; Name > > clay + Cs + acetate + water > > > > [ molecules ] > > ; Compound#mols > > UC21 > > UC11 > > UC3B 1 > > UC21 > > UC21 > > UC11 > > UC11 > > UC21 > > UC21 > > UC3T 1 > > UC11 > > UC21 > > UC21 > > UC3B 1 > > UC3T 1 > > UC21 > > UC21 > > UC11 > > UC3B 1 > > UC21 > > UC21 > > UC11 > > UC11 > > UC21 > > UC21 > > UC3T 1 > > UC11 > > UC21 > > UC21 > > UC3B 1 > > UC3T 1 > > UC2 1 > > Na 24 > > SOL 312 > > UC2 1 > > UC1 1 > > UC3B 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3T 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3B 1 > > UC3T 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC3B 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3T 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3B 1 > > UC3T 1 > > UC2 1 > > Na 24 > > SOL312 > > UC2 1 > > UC1 1 > > UC3B 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3T 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3B 1 > > UC3T 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC3B 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3T 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3B 1 > > UC3T 1 > > UC2 1 > > Na 24 > > Cs 16 > > act 16 > > SOL6103 > > > > *Step 3* > > In my mdp file, I defined it as follows: > > *define = -DPOSRES_Cs* > > > > > > *The problem : * > > gmx_mpi grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr > > > > Setting the LD random seed to 1967282441 > > Generated 83825 of the 83845 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 1 > > Generated 57459 of the 83845 1-4 parameter combinations > > > > ERROR 1 [file posres_Cs.itp, line 5]: > > Atom index (5790) in position_restraints out of bounds (1-1). > > This probably
Re: [gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?
On 5/5/20 5:54 PM, Debashish Banerjee wrote: Dear gmx users, I have been stuck in a problem for a month now and have scrutinized all the past discussions and forms related to it dating as back as 9 years. Now I really need your help. My system has Clays (layered philosillacates), Cesium ions (Cs), acetate molecules as well as water. In total 24241 atoms in the whole system. I want to perform free energy calculations *(PMF)* via *umbrella sampling*. The whole idea is that I want to fix one Cs atom (atom number/index number~ 5790) near to the basal surface (top layer) of clay and put in use of the* pull* code as described in umbrella sampling and thereafter perform *WHAM* calculations to see the progression of COM distance between (Cs) and the surface oxygen's present on the top layer of clay sheet over time. When, I see it in my .gro files, I can find all 16 Cs atoms ranging from index number (5785-5780). I just want to fix a particular single Cs atom (index number 5790) as mentioned above. For this I create a special index file which now has an extra group containing just 1 Cs atom. After this, I take in the use of gmx genrestr command : *gmx genrestr -f npt.gro -n index.ndx -o posre_Cs.itp -fc 0 0 1000* This commands redirects to the newly created group from the index file which I created above and put constraints in it. *Step 1 * The *posre_Cs.itp* file looks like this: [ position_restraints ] ; ifunct fcxfcyfcz 5790 1 00 1000 * Step 2 * *My topology should include an if statement, so I also define it like this:* #include "../charmm36.ff/forcefield.itp" ; include params for ClayFF #include "../ClayFF.ff/ffnonbonded.itp" ; Include topology for Clay Montmorillonite (MMT) #include "../ClayFF.ff/MMT_UC/UC2.itp" #include "../ClayFF.ff/MMT_UC/UC1.itp" #include "../ClayFF.ff/MMT_UC/UC3B.itp" #include "../ClayFF.ff/MMT_UC/UC3T.itp" ; Added the part of defining ions.itp which contains Cs atom and defined position restrain parameters *#include "../ClayFF.ff/ions.itp"#ifdef POSRES_Cs#include "posres_Cs.itp"#endif* #include "../charmm36.ff/spc.itp" #include "../charmm36.ff/organics/act.itp" [ system ] ; Name clay + Cs + acetate + water [ molecules ] ; Compound#mols UC21 UC11 UC3B 1 UC21 UC21 UC11 UC11 UC21 UC21 UC3T 1 UC11 UC21 UC21 UC3B 1 UC3T 1 UC21 UC21 UC11 UC3B 1 UC21 UC21 UC11 UC11 UC21 UC21 UC3T 1 UC11 UC21 UC21 UC3B 1 UC3T 1 UC2 1 Na 24 SOL 312 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 Na 24 SOL312 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 Na 24 Cs 16 act 16 SOL6103 *Step 3* In my mdp file, I defined it as follows: *define = -DPOSRES_Cs* *The problem : * gmx_mpi grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr Setting the LD random seed to 1967282441 Generated 83825 of the 83845 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 57459 of the 83845 1-4 parameter combinations ERROR 1 [file posres_Cs.itp, line 5]: Atom index (5790) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. http://manual.gromacs.org/current/user-guide/run-time-errors.html#atom-index-n-in-position-restraints-out-of-bounds Presumably your Cs+ topology defines the [moleculetype] as having one ion in it. Therefore, the only valid atom number in [position_restraints] is 1. The global atom numbering is meaningless in the context of position restraints (which are assigned at the topology level) as genrestr warns you (see the help description; if you're trying to restrain anything that isn't the first molecule, you can't use it). The solution is to define a new [moleculetype] for the Cs+ ion you want to restrain, and use [position_restraints] 1 1 0 0 1000 in its topology. -Justin --
Re: [gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?
Just a small rectification: *posres_Cs.itp* were created and used every time. I mistakenly wrote posre_Cs.itp while typing it here, my bad. Thanks, Debashish On Tue, May 5, 2020 at 11:54 PM Debashish Banerjee wrote: > Dear gmx users, > > I have been stuck in a problem for a month now and have scrutinized all > the past discussions and forms related to it dating as back as 9 years. Now > I really need your help. > > My system has Clays (layered philosillacates), Cesium ions (Cs), acetate > molecules as well as water. In total 24241 atoms in the whole system. I > want to perform free energy calculations *(PMF)* via *umbrella sampling*. > > The whole idea is that I want to fix one Cs atom (atom number/index > number~ 5790) near to the basal surface (top layer) of clay and put in use > of the* pull* code as described in umbrella sampling and thereafter > perform *WHAM* calculations to see the progression of COM distance > between (Cs) and the surface oxygen's present on the top layer of clay > sheet over time. > > When, I see it in my .gro files, I can find all 16 Cs atoms ranging from > index number (5785-5780). I just want to fix a particular single Cs atom > (index number 5790) as mentioned above. For this I create a special index > file which now has an extra group containing just 1 Cs atom. After this, I > take in the use of gmx genrestr command : > *gmx genrestr -f npt.gro -n index.ndx -o posre_Cs.itp -fc 0 0 1000* > This commands redirects to the newly created group from the index file > which I created above and put constraints in it. > > *Step 1 * > The *posre_Cs.itp* file looks like this: > [ position_restraints ] > ; ifunct fcxfcyfcz >5790 1 00 1000 > > * Step 2 * > *My topology should include an if statement, so I also define it like > this:* > > #include "../charmm36.ff/forcefield.itp" > > ; include params for ClayFF > #include "../ClayFF.ff/ffnonbonded.itp" > > ; Include topology for Clay Montmorillonite (MMT) > #include "../ClayFF.ff/MMT_UC/UC2.itp" > #include "../ClayFF.ff/MMT_UC/UC1.itp" > #include "../ClayFF.ff/MMT_UC/UC3B.itp" > #include "../ClayFF.ff/MMT_UC/UC3T.itp" > > ; Added the part of defining ions.itp which contains Cs atom and defined > position restrain parameters > > > > > *#include "../ClayFF.ff/ions.itp"#ifdef POSRES_Cs#include > "posres_Cs.itp"#endif* > #include "../charmm36.ff/spc.itp" > > #include "../charmm36.ff/organics/act.itp" > > [ system ] > ; Name > clay + Cs + acetate + water > > [ molecules ] > ; Compound#mols > UC21 > UC11 > UC3B 1 > UC21 > UC21 > UC11 > UC11 > UC21 > UC21 > UC3T 1 > UC11 > UC21 > UC21 > UC3B 1 > UC3T 1 > UC21 > UC21 > UC11 > UC3B 1 > UC21 > UC21 > UC11 > UC11 > UC21 > UC21 > UC3T 1 > UC11 > UC21 > UC21 > UC3B 1 > UC3T 1 > UC2 1 > Na 24 > SOL 312 > UC2 1 > UC1 1 > UC3B 1 > UC2 1 > UC2 1 > UC1 1 > UC1 1 > UC2 1 > UC2 1 > UC3T 1 > UC1 1 > UC2 1 > UC2 1 > UC3B 1 > UC3T 1 > UC2 1 > UC2 1 > UC1 1 > UC3B 1 > UC2 1 > UC2 1 > UC1 1 > UC1 1 > UC2 1 > UC2 1 > UC3T 1 > UC1 1 > UC2 1 > UC2 1 > UC3B 1 > UC3T 1 > UC2 1 > Na 24 > SOL312 > UC2 1 > UC1 1 > UC3B 1 > UC2 1 > UC2 1 > UC1 1 > UC1 1 > UC2 1 > UC2 1 > UC3T 1 > UC1 1 > UC2 1 > UC2 1 > UC3B 1 > UC3T 1 > UC2 1 > UC2 1 > UC1 1 > UC3B 1 > UC2 1 > UC2 1 > UC1 1 > UC1 1 > UC2 1 > UC2 1 > UC3T 1 > UC1 1 > UC2 1 > UC2 1 > UC3B 1 > UC3T 1 > UC2 1 > Na 24 > Cs 16 > act 16 > SOL6103 > > *Step 3* > In my mdp file, I defined it as follows: > *define = -DPOSRES_Cs* > > > *The problem : * > gmx_mpi grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr > > Setting the LD random seed to 1967282441 > Generated 83825 of the 83845 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 57459 of the 83845 1-4 parameter combinations > > ERROR 1 [file posres_Cs.itp, line 5]: > Atom index (5790) in position_restraints out of bounds (1-1). > This probably means that you have inserted topology section > "position_restraints" in a part belonging to a different molecule than > you intended to. > In that case move the "position_restraints" section to the right > molecule. > > There were 2 notes > --- > Program: gmx grompp, version 2016.4 > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1880) > >
[gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?
Dear gmx users, I have been stuck in a problem for a month now and have scrutinized all the past discussions and forms related to it dating as back as 9 years. Now I really need your help. My system has Clays (layered philosillacates), Cesium ions (Cs), acetate molecules as well as water. In total 24241 atoms in the whole system. I want to perform free energy calculations *(PMF)* via *umbrella sampling*. The whole idea is that I want to fix one Cs atom (atom number/index number~ 5790) near to the basal surface (top layer) of clay and put in use of the* pull* code as described in umbrella sampling and thereafter perform *WHAM* calculations to see the progression of COM distance between (Cs) and the surface oxygen's present on the top layer of clay sheet over time. When, I see it in my .gro files, I can find all 16 Cs atoms ranging from index number (5785-5780). I just want to fix a particular single Cs atom (index number 5790) as mentioned above. For this I create a special index file which now has an extra group containing just 1 Cs atom. After this, I take in the use of gmx genrestr command : *gmx genrestr -f npt.gro -n index.ndx -o posre_Cs.itp -fc 0 0 1000* This commands redirects to the newly created group from the index file which I created above and put constraints in it. *Step 1 * The *posre_Cs.itp* file looks like this: [ position_restraints ] ; ifunct fcxfcyfcz 5790 1 00 1000 * Step 2 * *My topology should include an if statement, so I also define it like this:* #include "../charmm36.ff/forcefield.itp" ; include params for ClayFF #include "../ClayFF.ff/ffnonbonded.itp" ; Include topology for Clay Montmorillonite (MMT) #include "../ClayFF.ff/MMT_UC/UC2.itp" #include "../ClayFF.ff/MMT_UC/UC1.itp" #include "../ClayFF.ff/MMT_UC/UC3B.itp" #include "../ClayFF.ff/MMT_UC/UC3T.itp" ; Added the part of defining ions.itp which contains Cs atom and defined position restrain parameters *#include "../ClayFF.ff/ions.itp"#ifdef POSRES_Cs#include "posres_Cs.itp"#endif* #include "../charmm36.ff/spc.itp" #include "../charmm36.ff/organics/act.itp" [ system ] ; Name clay + Cs + acetate + water [ molecules ] ; Compound#mols UC21 UC11 UC3B 1 UC21 UC21 UC11 UC11 UC21 UC21 UC3T 1 UC11 UC21 UC21 UC3B 1 UC3T 1 UC21 UC21 UC11 UC3B 1 UC21 UC21 UC11 UC11 UC21 UC21 UC3T 1 UC11 UC21 UC21 UC3B 1 UC3T 1 UC2 1 Na 24 SOL 312 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 Na 24 SOL312 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 Na 24 Cs 16 act 16 SOL6103 *Step 3* In my mdp file, I defined it as follows: *define = -DPOSRES_Cs* *The problem : * gmx_mpi grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr Setting the LD random seed to 1967282441 Generated 83825 of the 83845 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 57459 of the 83845 1-4 parameter combinations ERROR 1 [file posres_Cs.itp, line 5]: Atom index (5790) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. There were 2 notes --- Program: gmx grompp, version 2016.4 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1880) Fatal error: There was 1 error in input file(s) Kindly help me fix it please. With lots of hope of finding an answer -- *Best Regards* *Debashish Banerjee* *Ph.D. 3rd year (Nuclear Materials, Subatech)* *MS(Sustainable Nuclear Engineering)* *Advance Nuclear Waste Management* *Institut Mines-Telecom, **France* -- 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
Re: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis
On 5/5/20 12:12 PM, Neena Susan Eappen wrote: Thank you Sahil, I will try VMD plugin for H-bond analysis. Thank you Justin for your reply, it looks like gmx hbond considers only one N-H as donor when part of NH2 group. Please take a look at this file. This is what gmx hbond does by default, see gmx help hbond: -[no]merge (yes) H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF. This is a very different situation than claiming the NH2 group simply isn't accounted for. -Justin https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing Many thanks, Neena From: Neena Susan Eappen Sent: Tuesday, April 28, 2020 1:50 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx users] Terminal amide hydrogens not included in H-bond analysis Hello gromacs users, My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? Many thanks, Neena -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] apply protonation state CYS amino acid
On 5/4/20 11:46 PM, azadeh kordzadeh wrote: Hi Thank you very much for your answer to my former question I want to select CYSH state but we have this option for this amino acid. already I could determine especial state for his,lys,arg,asp by command -his but this command doesn't work for CYS Deprotonated (anionic) Cys is treated as a special residue by all force fields, usually something like CYM because it is not normally considered a titratable amino acid. Check the force field .rtp file and adjust the residue name accordingly. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] about how to create angle.index with specific angles
On 5/2/20 3:12 PM, lazaro monteserin wrote: Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (*dangle.ndx*) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before. 2) Then I extracted the sin/cos of the angles in the dangle.ndx from my MD in the file (*dangle.trr*) with the following command: *gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral* (I had 21 angles so it used 14 sin/cos to represent the angles) 3) Then I generated an index file (*covar.ndx*) with a list of numbers from 1 to 14 for trjconv. 4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis: *gmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 1* 1 was the time in ps for the last frame of the simulation. 5) I runned covar: *gmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc* 6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors: *gmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg* 7) Then I got the projection in 3D of the free energy landscape: *gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm* Note: I attached all the files in the dropbox link below https://www.dropbox.com/sh/wez43stnyv4ho31/AABQ3xwgUGf0CuMI_UF7MGsWa?dl=0 I can't access the Dropbox folder because you have given permission for the mailing list email to access it. Please either make it public or upload to a different service. The most relevant files are 2dproj_1_2.xvg and gibbs-1_2.xpm -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis
Thank you Sahil, I will try VMD plugin for H-bond analysis. Thank you Justin for your reply, it looks like gmx hbond considers only one N-H as donor when part of NH2 group. Please take a look at this file. https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing Many thanks, Neena From: Neena Susan Eappen Sent: Tuesday, April 28, 2020 1:50 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx users] Terminal amide hydrogens not included in H-bond analysis Hello gromacs users, My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? Many thanks, Neena -- 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] Size of Water Pools
Hi All, I am simulating systems with lipids, water and surfactants. I observed formation of water pools/water aggregates with different sizes in final frames. Now I want to measure size of these pools. What gromacs tool do you suggest me to use? I tried to do clustering first and thought calculating radius of gyration. However, clustering process takes ages to complete. Could you please help me to determine size of these water pools? Thank you. -- Best Regards Shan Jayasinghe -- 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.
