Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
On 8/2/17 9:12 AM, Ali Ahmed wrote: Dear all, Thank you for helping me. All I get from grompp is this -- gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o topol.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# NOTE 1 [file grompp.mdp]: The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators. Setting the LD random seed to 1000542586 Generated 120 of the 120 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 120 of the 120 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'N_2' Cleaning up constraints and constant bonded interactions with virtual sites Analysing residue names: There are: 2493 Other residues Simplify your system - work with one molecule and print out the forces at each step to see if there is something haywire going on. -Justin Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group System is 12462.00 NOTE 2 [file grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Largest charge group radii for Van der Waals: 0.056, 0.056 nm Largest charge group radii for Coulomb: 0.056, 0.056 nm This run will generate roughly 90 Mb of data There were 2 notes Back Off! I just backed up topol.tpr to ./#topol.tpr.1# gcq#454: "I never see what has been done; I only see what remains to be done." (Marie Curie) On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul wrote: On 8/1/17 6:07 PM, Ali Ahmed wrote: Dear Dr. Dallas, Thank you for your reply. Actually, I'm new to GROMACS and I appreciate your support. -- Here is what I get before crashing. Too many warning then crush. This is not diagnostic of anything useful. You've been asked several times to provide the output of grompp, not mdrun. The grompp output can be suggestive of issues you may not have considered. -Justin Step 37, time 0.037 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002768, max 0.195102 (between atoms 34930 and 34931) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 193194 51.70.1100 0.1100 0.1100 54409 54410 32.30.1100 0.1100 0.1100 On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren wrote: Copy the output from both of those commands, most importantly (as Mark has asked) that from the first one gmx grompp You need to show people exactly what you are seeing, not what you say you are seeing. The latter you are filtering it, and most likely not providing all the important information. The former allows those trying to help to see all the information that they need to see. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 2 August 2017 at 04:05, Ali Ahmed wrote: Hi, Thank you for your help. well I used this command gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em and I got all the warnings. Here is my em.mdp - integrator = steep emtol = 10.0 emstep = 0.001 nsteps = 5 energygrps = system ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 cutoff-scheme = group ns_type= grid coulombtype= PME rcoulomb = 1.0 rvdw= 1.0 pbc = xyz On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham wrote: Hi, No, only mdrun issues LINCS warnings. grompp issues different warnings, and I would like you to check whether you had any from grompp that you may not have considered. :-) Mark On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote: Dear Mark Yes, all the warnings are from grompp. I have no idea where is the problem in the structure or the topology Thank you On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham < mark.j.abra...@gmail.com> wrote: Hi, Did you get any warnings from grompp? Mark On Mon, Jul
Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
Dear all, Thank you for helping me. All I get from grompp is this -- gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o topol.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# NOTE 1 [file grompp.mdp]: The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators. Setting the LD random seed to 1000542586 Generated 120 of the 120 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 120 of the 120 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'N_2' Cleaning up constraints and constant bonded interactions with virtual sites Analysing residue names: There are: 2493 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group System is 12462.00 NOTE 2 [file grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Largest charge group radii for Van der Waals: 0.056, 0.056 nm Largest charge group radii for Coulomb: 0.056, 0.056 nm This run will generate roughly 90 Mb of data There were 2 notes Back Off! I just backed up topol.tpr to ./#topol.tpr.1# gcq#454: "I never see what has been done; I only see what remains to be done." (Marie Curie) On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul wrote: > > > On 8/1/17 6:07 PM, Ali Ahmed wrote: > >> Dear Dr. Dallas, >> Thank you for your reply. Actually, I'm new to GROMACS and >> I appreciate your support. >> >> >> -- >> Here is what I get before crashing. Too many warning then crush. >> >> > This is not diagnostic of anything useful. You've been asked several > times to provide the output of grompp, not mdrun. The grompp output can be > suggestive of issues you may not have considered. > > -Justin > > > Step 37, time 0.037 (ps) LINCS WARNING >> >> relative constraint deviation after LINCS: >> >> rms 0.002768, max 0.195102 (between atoms 34930 and 34931) >> >> bonds that rotated more than 30 degrees: >> >> atom 1 atom 2 angle previous, current, constraint length >> >> 193194 51.70.1100 0.1100 0.1100 >> >>54409 54410 32.30.1100 0.1100 0.1100 >> >> On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren >> wrote: >> >> Copy the output from both of those commands, most importantly (as Mark >>> has asked) that from the first one gmx grompp >>> >>> You need to show people exactly what you are seeing, not what you say >>> you are seeing. The latter you are filtering it, and most likely not >>> providing all the important information. The former allows those >>> trying to help to see all the information that they need to see. >>> Catch ya, >>> >>> Dr. Dallas Warren >>> Drug Delivery, Disposition and Dynamics >>> Monash Institute of Pharmaceutical Sciences, Monash University >>> 381 Royal Parade, Parkville VIC 3052 >>> dallas.war...@monash.edu >>> - >>> When the only tool you own is a hammer, every problem begins to resemble >>> a >>> nail. >>> >>> >>> On 2 August 2017 at 04:05, Ali Ahmed wrote: >>> Hi, Thank you for your help. well I used this command gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em and I got all the warnings. Here is my em.mdp >>> - >>> integrator = steep emtol = 10.0 emstep = 0.001 nsteps = 5 energygrps = system ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 cutoff-scheme = group ns_type= grid coulombtype= PME rcoulomb = 1.0 rvdw= 1.0 pbc = xyz On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham >>> > wrote: Hi, > > No, only mdrun issues LINCS warnings. grompp issues different warnings, > and >>> I would like you to check whether you had any from grompp that you may > not >>> have considered. :-) > > Mark > > On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote: > > Dear Mark >> Yes, all the warning
Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
On 8/1/17 6:07 PM, Ali Ahmed wrote: Dear Dr. Dallas, Thank you for your reply. Actually, I'm new to GROMACS and I appreciate your support. -- Here is what I get before crashing. Too many warning then crush. This is not diagnostic of anything useful. You've been asked several times to provide the output of grompp, not mdrun. The grompp output can be suggestive of issues you may not have considered. -Justin Step 37, time 0.037 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002768, max 0.195102 (between atoms 34930 and 34931) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 193194 51.70.1100 0.1100 0.1100 54409 54410 32.30.1100 0.1100 0.1100 On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren wrote: Copy the output from both of those commands, most importantly (as Mark has asked) that from the first one gmx grompp You need to show people exactly what you are seeing, not what you say you are seeing. The latter you are filtering it, and most likely not providing all the important information. The former allows those trying to help to see all the information that they need to see. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 2 August 2017 at 04:05, Ali Ahmed wrote: Hi, Thank you for your help. well I used this command gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em and I got all the warnings. Here is my em.mdp - integrator = steep emtol = 10.0 emstep = 0.001 nsteps = 5 energygrps = system ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 cutoff-scheme = group ns_type= grid coulombtype= PME rcoulomb = 1.0 rvdw= 1.0 pbc = xyz On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham wrote: Hi, No, only mdrun issues LINCS warnings. grompp issues different warnings, and I would like you to check whether you had any from grompp that you may not have considered. :-) Mark On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote: Dear Mark Yes, all the warnings are from grompp. I have no idea where is the problem in the structure or the topology Thank you On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham < mark.j.abra...@gmail.com> wrote: Hi, Did you get any warnings from grompp? Mark On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote: Hello GROMACS users, I'm doing MD for nitrogen, and for better electrostatic interactions I need to use massless and charged virtual site. I did that but when I try to do energy minimization gives me LINCS warning and crush. I don't know where is the error I tried a lot but could not find a solution. Anyone has an idea where is my error Here is the topology file (hand written) -- [ defaults ] 1 3 yes 0.5 0.5 ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon OP OP0.000 0.000A 0.330 0.3062 ; nitrogen M M 0.000 0.000V 0.000 0.000 ; virtual site [ moleculetype ] ; name nrexcl N2 2 [ atoms ] ; nr typeresnr residue atom cgnr charge mass 1 OP 1N2 N1 1-0.482 14.0067 2 M 1N2 M1 1 0.964 0.000 3 OP 1N2 N2 1-0.482 14.0067 [ constraints ] ; the N-N is fixed 1 3 1 0.11 [ virtual_sites2 ] ; site ai aj funct a 2 1 3 1 0.5000 ; right in the mid [ system ] N2 in vacuo [ molecules ] N2 1500 -- Here is the structure (N2.pdb) --- TITLE N2 with dummy masses REMARKTHIS IS A SIMULATION BOX MODEL1 COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.2 CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00 0.00 N ATOM
Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
Dear Dr. Dallas, Thank you for your reply. Actually, I'm new to GROMACS and I appreciate your support. -- Here is what I get before crashing. Too many warning then crush. Step 37, time 0.037 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002768, max 0.195102 (between atoms 34930 and 34931) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 193194 51.70.1100 0.1100 0.1100 54409 54410 32.30.1100 0.1100 0.1100 On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren wrote: > Copy the output from both of those commands, most importantly (as Mark > has asked) that from the first one gmx grompp > > You need to show people exactly what you are seeing, not what you say > you are seeing. The latter you are filtering it, and most likely not > providing all the important information. The former allows those > trying to help to see all the information that they need to see. > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 2 August 2017 at 04:05, Ali Ahmed wrote: > > Hi, > > Thank you for your help. > > > > well I used this command > > > > gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr > > gmx mdrun -v -deffnm em > > > > and I got all the warnings. Here is my em.mdp > > > - > > > > integrator = steep > > > > emtol = 10.0 > > > > emstep = 0.001 > > > > nsteps = 5 > > > > energygrps = system > > > > ; Parameters describing how to find the neighbors of each atom and how to > > calculate the interactions > > > > nstlist = 1 > > > > cutoff-scheme = group > > > > ns_type= grid > > > > coulombtype= PME > > > > rcoulomb = 1.0 > > > > rvdw= 1.0 > > > > pbc = xyz > > > > On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham > > wrote: > > > >> Hi, > >> > >> No, only mdrun issues LINCS warnings. grompp issues different warnings, > and > >> I would like you to check whether you had any from grompp that you may > not > >> have considered. :-) > >> > >> Mark > >> > >> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote: > >> > >> > Dear Mark > >> > Yes, all the warnings are from grompp. > >> > I have no idea where is the problem in the structure or the topology > >> > Thank you > >> > > >> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham < > mark.j.abra...@gmail.com> > >> > wrote: > >> > > >> > > Hi, > >> > > > >> > > Did you get any warnings from grompp? > >> > > > >> > > Mark > >> > > > >> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed > wrote: > >> > > > >> > > > Hello GROMACS users, > >> > > > > >> > > > I'm doing MD for nitrogen, and for better electrostatic > interactions > >> I > >> > > need > >> > > > to use massless and charged virtual site. I did that but when I > try > >> to > >> > do > >> > > > energy minimization gives me LINCS warning and crush. I don't know > >> > where > >> > > is > >> > > > the error I tried a lot but could not find a solution. > >> > > > Anyone has an idea where is my error > >> > > > > >> > > > Here is the topology file (hand written) > >> > > > > >> > > > -- > >> > > > > >> > > > [ defaults ] > >> > > > > >> > > > 1 3 yes 0.5 0.5 > >> > > > > >> > > > > >> > > ; > >> > > > > >> > > > [ atomtypes ] > >> > > > > >> > > > ; name bond_typemasscharge ptype sigma > >> epsilon > >> > > > > >> > > > OP OP0.000 0.000A 0.330 > >> 0.3062 > >> > ; > >> > > > nitrogen > >> > > > > >> > > > M M 0.000 0.000V 0.000 > >> > 0.000 > >> > > ; > >> > > > virtual site > >> > > > > >> > > > > >> > > > > >> > > > >> > > > > >> > > > [ moleculetype ] > >> > > > > >> > > > ; name nrexcl > >> > > > > >> > > > N2 2 > >> > > > > >> > > > > >> > > > > >> > > > [ atoms ] > >> > > > > >> > > > ; nr typeresnr residue atom cgnr charge mass > >> > > > > >> > > > 1 OP 1N2 N1 1-0.482 > 14.0067 > >> > > > > >> > > > 2 M 1N2 M1 1 0.964 0.000 > >> > > > > >> > > > 3 OP 1N2 N2 1-0.482 > 14.0067 > >> > > > > >> > > > > >> > > > > >> > > > [ constrai
Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
Copy the output from both of those commands, most importantly (as Mark has asked) that from the first one gmx grompp You need to show people exactly what you are seeing, not what you say you are seeing. The latter you are filtering it, and most likely not providing all the important information. The former allows those trying to help to see all the information that they need to see. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 2 August 2017 at 04:05, Ali Ahmed wrote: > Hi, > Thank you for your help. > > well I used this command > > gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr > gmx mdrun -v -deffnm em > > and I got all the warnings. Here is my em.mdp > - > > integrator = steep > > emtol = 10.0 > > emstep = 0.001 > > nsteps = 5 > > energygrps = system > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > > nstlist = 1 > > cutoff-scheme = group > > ns_type= grid > > coulombtype= PME > > rcoulomb = 1.0 > > rvdw= 1.0 > > pbc = xyz > > On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham > wrote: > >> Hi, >> >> No, only mdrun issues LINCS warnings. grompp issues different warnings, and >> I would like you to check whether you had any from grompp that you may not >> have considered. :-) >> >> Mark >> >> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote: >> >> > Dear Mark >> > Yes, all the warnings are from grompp. >> > I have no idea where is the problem in the structure or the topology >> > Thank you >> > >> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham >> > wrote: >> > >> > > Hi, >> > > >> > > Did you get any warnings from grompp? >> > > >> > > Mark >> > > >> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote: >> > > >> > > > Hello GROMACS users, >> > > > >> > > > I'm doing MD for nitrogen, and for better electrostatic interactions >> I >> > > need >> > > > to use massless and charged virtual site. I did that but when I try >> to >> > do >> > > > energy minimization gives me LINCS warning and crush. I don't know >> > where >> > > is >> > > > the error I tried a lot but could not find a solution. >> > > > Anyone has an idea where is my error >> > > > >> > > > Here is the topology file (hand written) >> > > > >> > > > -- >> > > > >> > > > [ defaults ] >> > > > >> > > > 1 3 yes 0.5 0.5 >> > > > >> > > > >> > > ; >> > > > >> > > > [ atomtypes ] >> > > > >> > > > ; name bond_typemasscharge ptype sigma >> epsilon >> > > > >> > > > OP OP0.000 0.000A 0.330 >> 0.3062 >> > ; >> > > > nitrogen >> > > > >> > > > M M 0.000 0.000V 0.000 >> > 0.000 >> > > ; >> > > > virtual site >> > > > >> > > > >> > > > >> > > >> > > > >> > > > [ moleculetype ] >> > > > >> > > > ; name nrexcl >> > > > >> > > > N2 2 >> > > > >> > > > >> > > > >> > > > [ atoms ] >> > > > >> > > > ; nr typeresnr residue atom cgnr charge mass >> > > > >> > > > 1 OP 1N2 N1 1-0.482 14.0067 >> > > > >> > > > 2 M 1N2 M1 1 0.964 0.000 >> > > > >> > > > 3 OP 1N2 N2 1-0.482 14.0067 >> > > > >> > > > >> > > > >> > > > [ constraints ] >> > > > >> > > > ; the N-N is fixed >> > > > >> > > > 1 3 1 0.11 >> > > > >> > > > >> > > > >> > > > [ virtual_sites2 ] >> > > > >> > > > ; site ai aj funct a >> > > > >> > > > 2 1 3 1 0.5000 ; right in the mid >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > [ system ] >> > > > >> > > > N2 in vacuo >> > > > >> > > > >> > > > >> > > > [ molecules ] >> > > > >> > > > N2 1500 >> > > > >> > > > >> > > > -- >> > > > >> > > > Here is the structure (N2.pdb) >> > > > >> > > > --- >> > > > >> > > > TITLE N2 with dummy masses >> > > > >> > > > REMARKTHIS IS A SIMULATION BOX >> > > > >> > > > MODEL1 >> > > > >> > > > COMPNDUNNAMED >> > > > >> > > > AUTHORGENERATED BY OPEN BABEL 2.3.2 >> > > > >> > > > CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 >> > > > >> > > > ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00 >> > > > 0
Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
Hi, Thank you for your help. well I used this command gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em and I got all the warnings. Here is my em.mdp - integrator = steep emtol = 10.0 emstep = 0.001 nsteps = 5 energygrps = system ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 cutoff-scheme = group ns_type= grid coulombtype= PME rcoulomb = 1.0 rvdw= 1.0 pbc = xyz On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham wrote: > Hi, > > No, only mdrun issues LINCS warnings. grompp issues different warnings, and > I would like you to check whether you had any from grompp that you may not > have considered. :-) > > Mark > > On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote: > > > Dear Mark > > Yes, all the warnings are from grompp. > > I have no idea where is the problem in the structure or the topology > > Thank you > > > > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > Did you get any warnings from grompp? > > > > > > Mark > > > > > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote: > > > > > > > Hello GROMACS users, > > > > > > > > I'm doing MD for nitrogen, and for better electrostatic interactions > I > > > need > > > > to use massless and charged virtual site. I did that but when I try > to > > do > > > > energy minimization gives me LINCS warning and crush. I don't know > > where > > > is > > > > the error I tried a lot but could not find a solution. > > > > Anyone has an idea where is my error > > > > > > > > Here is the topology file (hand written) > > > > > > > > -- > > > > > > > > [ defaults ] > > > > > > > > 1 3 yes 0.5 0.5 > > > > > > > > > > > ; > > > > > > > > [ atomtypes ] > > > > > > > > ; name bond_typemasscharge ptype sigma > epsilon > > > > > > > > OP OP0.000 0.000A 0.330 > 0.3062 > > ; > > > > nitrogen > > > > > > > > M M 0.000 0.000V 0.000 > > 0.000 > > > ; > > > > virtual site > > > > > > > > > > > > > > > > > > > > > > > [ moleculetype ] > > > > > > > > ; name nrexcl > > > > > > > > N2 2 > > > > > > > > > > > > > > > > [ atoms ] > > > > > > > > ; nr typeresnr residue atom cgnr charge mass > > > > > > > > 1 OP 1N2 N1 1-0.482 14.0067 > > > > > > > > 2 M 1N2 M1 1 0.964 0.000 > > > > > > > > 3 OP 1N2 N2 1-0.482 14.0067 > > > > > > > > > > > > > > > > [ constraints ] > > > > > > > > ; the N-N is fixed > > > > > > > > 1 3 1 0.11 > > > > > > > > > > > > > > > > [ virtual_sites2 ] > > > > > > > > ; site ai aj funct a > > > > > > > > 2 1 3 1 0.5000 ; right in the mid > > > > > > > > > > > > > > > > > > > > > > > > [ system ] > > > > > > > > N2 in vacuo > > > > > > > > > > > > > > > > [ molecules ] > > > > > > > > N2 1500 > > > > > > > > > > > > -- > > > > > > > > Here is the structure (N2.pdb) > > > > > > > > --- > > > > > > > > TITLE N2 with dummy masses > > > > > > > > REMARKTHIS IS A SIMULATION BOX > > > > > > > > MODEL1 > > > > > > > > COMPNDUNNAMED > > > > > > > > AUTHORGENERATED BY OPEN BABEL 2.3.2 > > > > > > > > CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 > > > > > > > > ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00 > > > > 0.00 N > > > > > > > > ATOM 2 M1 N2 1 0.55000 0.000 0.000 1.00 > > > > 0.00 Xx > > > > > > > > ATOM 3 N2 N2 1 1.100 0.000 0.000 1.00 > > > > 0.00 N > > > > > > > > CONECT13 > > > > > > > > CONECT31 > > > > > > > > MASTER00000000303 > 0 > > > > > > > > END0 > > > > > > > > > > > > - > > > > 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
Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
Hi, No, only mdrun issues LINCS warnings. grompp issues different warnings, and I would like you to check whether you had any from grompp that you may not have considered. :-) Mark On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote: > Dear Mark > Yes, all the warnings are from grompp. > I have no idea where is the problem in the structure or the topology > Thank you > > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham > wrote: > > > Hi, > > > > Did you get any warnings from grompp? > > > > Mark > > > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote: > > > > > Hello GROMACS users, > > > > > > I'm doing MD for nitrogen, and for better electrostatic interactions I > > need > > > to use massless and charged virtual site. I did that but when I try to > do > > > energy minimization gives me LINCS warning and crush. I don't know > where > > is > > > the error I tried a lot but could not find a solution. > > > Anyone has an idea where is my error > > > > > > Here is the topology file (hand written) > > > > > > -- > > > > > > [ defaults ] > > > > > > 1 3 yes 0.5 0.5 > > > > > > > > ; > > > > > > [ atomtypes ] > > > > > > ; name bond_typemasscharge ptype sigma epsilon > > > > > > OP OP0.000 0.000A 0.330 0.3062 > ; > > > nitrogen > > > > > > M M 0.000 0.000V 0.000 > 0.000 > > ; > > > virtual site > > > > > > > > > > > > > > > > > [ moleculetype ] > > > > > > ; name nrexcl > > > > > > N2 2 > > > > > > > > > > > > [ atoms ] > > > > > > ; nr typeresnr residue atom cgnr charge mass > > > > > > 1 OP 1N2 N1 1-0.482 14.0067 > > > > > > 2 M 1N2 M1 1 0.964 0.000 > > > > > > 3 OP 1N2 N2 1-0.482 14.0067 > > > > > > > > > > > > [ constraints ] > > > > > > ; the N-N is fixed > > > > > > 1 3 1 0.11 > > > > > > > > > > > > [ virtual_sites2 ] > > > > > > ; site ai aj funct a > > > > > > 2 1 3 1 0.5000 ; right in the mid > > > > > > > > > > > > > > > > > > [ system ] > > > > > > N2 in vacuo > > > > > > > > > > > > [ molecules ] > > > > > > N2 1500 > > > > > > > > > -- > > > > > > Here is the structure (N2.pdb) > > > > > > --- > > > > > > TITLE N2 with dummy masses > > > > > > REMARKTHIS IS A SIMULATION BOX > > > > > > MODEL1 > > > > > > COMPNDUNNAMED > > > > > > AUTHORGENERATED BY OPEN BABEL 2.3.2 > > > > > > CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 > > > > > > ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00 > > > 0.00 N > > > > > > ATOM 2 M1 N2 1 0.55000 0.000 0.000 1.00 > > > 0.00 Xx > > > > > > ATOM 3 N2 N2 1 1.100 0.000 0.000 1.00 > > > 0.00 N > > > > > > CONECT13 > > > > > > CONECT31 > > > > > > MASTER000000003030 > > > > > > END0 > > > > > > > > > - > > > 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. > > > -- > 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/gro
Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
Dear Mark Yes, all the warnings are from grompp. I have no idea where is the problem in the structure or the topology Thank you On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham wrote: > Hi, > > Did you get any warnings from grompp? > > Mark > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote: > > > Hello GROMACS users, > > > > I'm doing MD for nitrogen, and for better electrostatic interactions I > need > > to use massless and charged virtual site. I did that but when I try to do > > energy minimization gives me LINCS warning and crush. I don't know where > is > > the error I tried a lot but could not find a solution. > > Anyone has an idea where is my error > > > > Here is the topology file (hand written) > > > > -- > > > > [ defaults ] > > > > 1 3 yes 0.5 0.5 > > > > > ; > > > > [ atomtypes ] > > > > ; name bond_typemasscharge ptype sigma epsilon > > > > OP OP0.000 0.000A 0.330 0.3062 ; > > nitrogen > > > > M M 0.000 0.000V 0.000 0.000 > ; > > virtual site > > > > > > > > > > > [ moleculetype ] > > > > ; name nrexcl > > > > N2 2 > > > > > > > > [ atoms ] > > > > ; nr typeresnr residue atom cgnr charge mass > > > > 1 OP 1N2 N1 1-0.482 14.0067 > > > > 2 M 1N2 M1 1 0.964 0.000 > > > > 3 OP 1N2 N2 1-0.482 14.0067 > > > > > > > > [ constraints ] > > > > ; the N-N is fixed > > > > 1 3 1 0.11 > > > > > > > > [ virtual_sites2 ] > > > > ; site ai aj funct a > > > > 2 1 3 1 0.5000 ; right in the mid > > > > > > > > > > > > [ system ] > > > > N2 in vacuo > > > > > > > > [ molecules ] > > > > N2 1500 > > > > > > -- > > > > Here is the structure (N2.pdb) > > > > --- > > > > TITLE N2 with dummy masses > > > > REMARKTHIS IS A SIMULATION BOX > > > > MODEL1 > > > > COMPNDUNNAMED > > > > AUTHORGENERATED BY OPEN BABEL 2.3.2 > > > > CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 > > > > ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00 > > 0.00 N > > > > ATOM 2 M1 N2 1 0.55000 0.000 0.000 1.00 > > 0.00 Xx > > > > ATOM 3 N2 N2 1 1.100 0.000 0.000 1.00 > > 0.00 N > > > > CONECT13 > > > > CONECT31 > > > > MASTER000000003030 > > > > END0 > > > > > > - > > 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. > -- 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] LINCS warning during energy minimization of nitrogen with virtual site
Hi, Did you get any warnings from grompp? Mark On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote: > Hello GROMACS users, > > I'm doing MD for nitrogen, and for better electrostatic interactions I need > to use massless and charged virtual site. I did that but when I try to do > energy minimization gives me LINCS warning and crush. I don't know where is > the error I tried a lot but could not find a solution. > Anyone has an idea where is my error > > Here is the topology file (hand written) > > -- > > [ defaults ] > > 1 3 yes 0.5 0.5 > > ; > > [ atomtypes ] > > ; name bond_typemasscharge ptype sigma epsilon > > OP OP0.000 0.000A 0.330 0.3062 ; > nitrogen > > M M 0.000 0.000V 0.000 0.000 ; > virtual site > > > > > [ moleculetype ] > > ; name nrexcl > > N2 2 > > > > [ atoms ] > > ; nr typeresnr residue atom cgnr charge mass > > 1 OP 1N2 N1 1-0.482 14.0067 > > 2 M 1N2 M1 1 0.964 0.000 > > 3 OP 1N2 N2 1-0.482 14.0067 > > > > [ constraints ] > > ; the N-N is fixed > > 1 3 1 0.11 > > > > [ virtual_sites2 ] > > ; site ai aj funct a > > 2 1 3 1 0.5000 ; right in the mid > > > > > > [ system ] > > N2 in vacuo > > > > [ molecules ] > > N2 1500 > > > -- > > Here is the structure (N2.pdb) > > --- > > TITLE N2 with dummy masses > > REMARKTHIS IS A SIMULATION BOX > > MODEL1 > > COMPNDUNNAMED > > AUTHORGENERATED BY OPEN BABEL 2.3.2 > > CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 > > ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00 > 0.00 N > > ATOM 2 M1 N2 1 0.55000 0.000 0.000 1.00 > 0.00 Xx > > ATOM 3 N2 N2 1 1.100 0.000 0.000 1.00 > 0.00 N > > CONECT13 > > CONECT31 > > MASTER000000003030 > > END0 > > > - > 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] LINCS warning during energy minimization of nitrogen with virtual site
Hello GROMACS users, I'm doing MD for nitrogen, and for better electrostatic interactions I need to use massless and charged virtual site. I did that but when I try to do energy minimization gives me LINCS warning and crush. I don't know where is the error I tried a lot but could not find a solution. Anyone has an idea where is my error Here is the topology file (hand written) -- [ defaults ] 1 3 yes 0.5 0.5 ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon OP OP0.000 0.000A 0.330 0.3062 ; nitrogen M M 0.000 0.000V 0.000 0.000 ; virtual site [ moleculetype ] ; name nrexcl N2 2 [ atoms ] ; nr typeresnr residue atom cgnr charge mass 1 OP 1N2 N1 1-0.482 14.0067 2 M 1N2 M1 1 0.964 0.000 3 OP 1N2 N2 1-0.482 14.0067 [ constraints ] ; the N-N is fixed 1 3 1 0.11 [ virtual_sites2 ] ; site ai aj funct a 2 1 3 1 0.5000 ; right in the mid [ system ] N2 in vacuo [ molecules ] N2 1500 -- Here is the structure (N2.pdb) --- TITLE N2 with dummy masses REMARKTHIS IS A SIMULATION BOX MODEL1 COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.2 CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00 0.00 N ATOM 2 M1 N2 1 0.55000 0.000 0.000 1.00 0.00 Xx ATOM 3 N2 N2 1 1.100 0.000 0.000 1.00 0.00 N CONECT13 CONECT31 MASTER000000003030 END0 - 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.