Re: [gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?
Hello gmx users, I am stuck at a very basic command line and need your expertise in dealing through it. Basically, I have a clay sheet containing 192 surface oxygen. Since I am doing umbrella sampling for PMF calculations, I want to get the progression of COM distances of my fixed Cs atom from the center of mass of the clay sheet (basically these 192 surface oxygen) over time. I have already created special index file which has relevant groups such as ; group 18 --> *referenceSurface* ~containing 192 surface oxygen group 19 --> *restrainedCs* ~containing 1 Cs atom (basically the one that I have fixed) group 20 --> another Cs atom (this one is not fixed and can move freely in all sample space during the entire course of simulation) Command line: *Case 1* *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of group 19 plus com of group 18' -oxyz dist00.xvg* Inconsistency in user input: Invalid index group reference(s) Group 'referenceSurface' cannot be used in selections except as a full value of the selection, because atom indices in it are not sorted and/or it contains duplicate atoms. *Case 2* *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of group 19 plus com of group 20' -oxyz dist2.xvg* Reading file npt.tpr, VERSION 2016.4 (single precision) Reading frames from gro file 'Generated by trjconv : clay + Cs + acetate + water t= 2.0', 24221 atoms. Last frame 0 time2.000 Analyzed 1 frames, last time 2.000 com of group 19 plus com of group 20: Number of samples: 1 Average distance: 0.52370 nm Standard deviation: 0.0 nm My understanding is that if I compare the above 2 cases, I would say that for *case 2*, Cs is measuring it's distance from the only other Cs atom. No problem here, whereas for *case 1*, Cs atom is measuring it's distance from all 192 oxygen atoms, somehow not understanding how to take the center of mass of the whole sheet containing 192 atoms. Approach taken: 1. Modified my command line from this: gmx_mpi distance -s pull.tpr -f conf0.gro -n index.ndx -select 'com of group "restrainedCs" plus com of group "referenceSurface"' -oall dist0.xvg 2. Used all output options like -oav / -oxyz I have followed the following threads, but still couldn't manage to rectify this error https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg16576.html https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg30552.html Please help. I am pretty much sure that I am overseeing a very basic step. Regards, Debashish On Wed, May 6, 2020 at 12:40 AM Debashish Banerjee wrote: > 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
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
