Re: [gmx-users] dna and cnt get distorted in md simulation
Okay, thank you very much. Sounds very plausibly, I will look up the .itp files for bonded interactions of CNT. Thanks, Majid From: Justin A. Lemkul To: Gromacs Users' List Sent: Thu, April 21, 2011 12:01:46 PM Subject: Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: > Okay, so here is the file that I used for both energy minimization (with >integrator = l-bfgs), and MD (integrator = md). Everything other than the >value >of integrator was same for both energy minimization and MD. > http://phas.ubc.ca/~majid/md.mdp > > and here is what I see by running .trr files obtained from EM, and MD. > > On running EM.trr file: > In the beginning of simulation, DNA is very stretched i.e atoms of DNA are >widely separated from each other, and CNT crumples. Then, gradually DNA >shrinks >and converges onto CNT. > OK, so the DNA is experiencing the charge repulsion I described earlier. The CNT sounds like it does not have proper bonded interactions assigned. > On running MD.trr file: > CNT suddenly moves toward and DNA and one part is mixed with DNA and whole >structure is crumpled (similar to the final state of EM.trr simulation). Then >this crumpled structure wiggles around until the end of simulation. > If EM is showing such weird results, then you can't really trust anything you see in the MD afterwards. > > Yes, I ran the whole process in vacuum. I am going to do this simulation by >changing cutoff to shift, and see which one works better, and then I will do >it >with a solvent. > There is no point in making this assessment in vacuo and then transferring it to solution. Plain cutoffs should not be used. Their artifacts are well-known and modern simulations should not use them. Shifted functions have discontinuities at their longest cutoff and neglect electrostatic interactions beyond this cutoff. Your best option in solution (especially for highly-charged molecules like DNA) is PME. -Justin > Thanks, > Majid > > *From:* Justin A. Lemkul > *To:* Gromacs Users' List > *Sent:* Thu, April 21, 2011 10:25:35 AM > *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation > > > > majid hasan wrote: > > first .mdp file is the original one, and modified .mdp is the one where I >made modifications, and I have tried both, and both lead to stable structures >for individual molecules, and distorted structures for combined system. > > > > The reason I asked is that the two are very different - one is for MD and the >other is for EM, and in some cases, many of the options are irrelevant for >either process so it is somewhat hard to deduce what you're actually trying to >accomplish with each, especially given the differences. It is best to only >post >the actual .mdp files you're using and a description of the output >corresponding >to each. > > > In the first .mdp file, free energy calculations are turned off, but even >with this file, I get huge distortions in the shape of molecules. > > So, the "first" .mdp file is the one that actually specifies an MD run, not >EM? Or does "first" correspond to the order of the workflow? It might be >best >to focus on one process at a time, rather than trying to troubleshoot both EM >and MD with some arbitrary designators. > > > CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. > > Bonds don't break or form during classical MD. Any bonds "forming" or >"breaking" are simply a visualization artifact since you're not reading a >topology into the visualization software. > > From your description, it sounds like these simulations are being conducted > in >vacuo? I tend to suspect that is the source of the problems. Plain cutoffs >for >electrostatics lead to nasty artifacts and the presence of a highly charged >molecule (DNA) that has no shielding between these charges is quite likely to >become very distorted due to its own intrinsic repulsion. > > -Justin > > > Thank You, > > Majid > > > > > > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>> > > *To:* Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>> > > *Sent:* Thu, April 21, 2011 4:02:57 AM > > *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation > > > > > > > > majid hasan wrote: > > > Dear All, > > > > > > I minimized the energy of my CNT-
Re: [gmx-users] dna and cnt get distorted in md simulation
majid hasan wrote: Okay, so here is the file that I used for both energy minimization (with integrator = l-bfgs), and MD (integrator = md). Everything other than the value of integrator was same for both energy minimization and MD. http://phas.ubc.ca/~majid/md.mdp and here is what I see by running .trr files obtained from EM, and MD. On running EM.trr file: In the beginning of simulation, DNA is very stretched i.e atoms of DNA are widely separated from each other, and CNT crumples. Then, gradually DNA shrinks and converges onto CNT. OK, so the DNA is experiencing the charge repulsion I described earlier. The CNT sounds like it does not have proper bonded interactions assigned. On running MD.trr file: CNT suddenly moves toward and DNA and one part is mixed with DNA and whole structure is crumpled (similar to the final state of EM.trr simulation). Then this crumpled structure wiggles around until the end of simulation. If EM is showing such weird results, then you can't really trust anything you see in the MD afterwards. Yes, I ran the whole process in vacuum. I am going to do this simulation by changing cutoff to shift, and see which one works better, and then I will do it with a solvent. There is no point in making this assessment in vacuo and then transferring it to solution. Plain cutoffs should not be used. Their artifacts are well-known and modern simulations should not use them. Shifted functions have discontinuities at their longest cutoff and neglect electrostatic interactions beyond this cutoff. Your best option in solution (especially for highly-charged molecules like DNA) is PME. -Justin Thanks, Majid *From:* Justin A. Lemkul *To:* Gromacs Users' List *Sent:* Thu, April 21, 2011 10:25:35 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: > first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. > The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each. > In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. So, the "first" .mdp file is the one that actually specifies an MD run, not EM? Or does "first" correspond to the order of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators. > CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Bonds don't break or form during classical MD. Any bonds "forming" or "breaking" are simply a visualization artifact since you're not reading a topology into the visualization software. From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion. -Justin > Thank You, > Majid > > > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>> > *To:* Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>> > *Sent:* Thu, April 21, 2011 4:02:57 AM > *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation > > > > majid hasan wrote: > > Dear All, > > > > I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. > > My commands are: > > For energy minimization, > > > > grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 > > mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd > > > > and then I ran molecular dyamics, > > > > grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 > > mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd > > > > For ind
Re: [gmx-users] dna and cnt get distorted in md simulation
Okay, so here is the file that I used for both energy minimization (with integrator = l-bfgs), and MD (integrator = md). Everything other than the value of integrator was same for both energy minimization and MD. http://phas.ubc.ca/~majid/md.mdp and here is what I see by running .trr files obtained from EM, and MD. On running EM.trr file: In the beginning of simulation, DNA is very stretched i.e atoms of DNA are widely separated from each other, and CNT crumples. Then, gradually DNA shrinks and converges onto CNT. On running MD.trr file: CNT suddenly moves toward and DNA and one part is mixed with DNA and whole structure is crumpled (similar to the final state of EM.trr simulation). Then this crumpled structure wiggles around until the end of simulation. Yes, I ran the whole process in vacuum. I am going to do this simulation by changing cutoff to shift, and see which one works better, and then I will do it with a solvent. Thanks, Majid From: Justin A. Lemkul To: Gromacs Users' List Sent: Thu, April 21, 2011 10:25:35 AM Subject: Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: > first .mdp file is the original one, and modified .mdp is the one where I > made >modifications, and I have tried both, and both lead to stable structures for >individual molecules, and distorted structures for combined system. > The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each. > In the first .mdp file, free energy calculations are turned off, but even > with >this file, I get huge distortions in the shape of molecules. > So, the "first" .mdp file is the one that actually specifies an MD run, not EM? Or does "first" correspond to the order of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators. > CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Bonds don't break or form during classical MD. Any bonds "forming" or "breaking" are simply a visualization artifact since you're not reading a topology into the visualization software. >From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion. -Justin > Thank You, > Majid > > > *From:* Justin A. Lemkul > *To:* Discussion list for GROMACS users > *Sent:* Thu, April 21, 2011 4:02:57 AM > *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation > > > > majid hasan wrote: > > Dear All, > > > > I minimized the energy of my CNT-DNA system with l-bfgs integrator, and > then >ran the mdrun with integrator = md. I am using a small ssDNA consisting of two >residues only (66 atoms), and a small CNT of about 80 atoms. > > My commands are: > > For energy minimization, > > > > grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr > -maxwarn >20 > > mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd > > > > and then I ran molecular dyamics, > > > > grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 > > mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd > > > > For individual DNA, and CNT alone, both produce reasonable results, where >molecule stays together and jiggles around. However on combining the two >molecules, both energy minimization and mdrun lead to distorted structures: >bond >lengths don't remain fixed neither for CNT nor for DNA, and atoms of both >molecules get intertwined and produce a mess. I tried two .mdp files. > > I got the first .mdp from a colleague who used it for a simple simulation >of CNT only (without solvent, and any other molecule) . I made few changes in >this file after going through manual e.g enabled free energy calculations, >added >"nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, >changed "ns_type" value from grid to simple, changed &
Re: [gmx-users] dna and cnt get distorted in md simulation
majid hasan wrote: first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. So, the "first" .mdp file is the one that actually specifies an MD run, not EM? Or does "first" correspond to the order of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Bonds don't break or form during classical MD. Any bonds "forming" or "breaking" are simply a visualization artifact since you're not reading a topology into the visualization software. From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion. -Justin Thank You, Majid *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Thu, April 21, 2011 4:02:57 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: > Dear All, > > I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. > My commands are: > For energy minimization, > > grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 > mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd > > and then I ran molecular dyamics, > > grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 > mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd > > For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. > I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added "nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, changed "ns_type" value from grid to simple, changed "rcoulomb" and "rvdw" values from 0.9 to 1, > Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one. http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) > > It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. Why are you employing the free energy code? It seems to me this could be the source of your problems. Each molecule alone is fine, but then by decoupling van der Waals and Coulombic interactions between them, you could be getting instability. Turn off the free energy options and see if you get stable trajectories. -Justin > Thanks, > Majid > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org <mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo
Re: [gmx-users] dna and cnt get distorted in md simulation
first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Thank You, Majid From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Thu, April 21, 2011 4:02:57 AM Subject: Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: > Dear All, > > I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then >ran the mdrun with integrator = md. I am using a small ssDNA consisting of two >residues only (66 atoms), and a small CNT of about 80 atoms. > > My commands are: > For energy minimization, > > grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 > mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd > > and then I ran molecular dyamics, > > grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 > mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd > > For individual DNA, and CNT alone, both produce reasonable results, where >molecule stays together and jiggles around. However on combining the two >molecules, both energy minimization and mdrun lead to distorted structures: >bond >lengths don't remain fixed neither for CNT nor for DNA, and atoms of both >molecules get intertwined and produce a mess. I tried two .mdp files. > > I got the first .mdp from a colleague who used it for a simple simulation of >CNT only (without solvent, and any other molecule) . I made few changes in >this >file after going through manual e.g enabled free energy calculations, added >"nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, >changed "ns_type" value from grid to simple, changed "rcoulomb" and "rvdw" >values from 0.9 to 1, > Both .mdp files are placed at following addresses: > http://phas.ubc.ca/~majid/md.mdp (first .mdp file) Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one. > http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) > > It seems to me that problem might be related to non-bonded interaction > because >this is the significant difference between one and two molecule system. Any >help >would be much appreciated. > Why are you employing the free energy code? It seems to me this could be the source of your problems. Each molecule alone is fine, but then by decoupling van der Waals and Coulombic interactions between them, you could be getting instability. Turn off the free energy options and see if you get stable trajectories. -Justin > Thanks, > Majid > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dna and cnt get distorted in md simulation
majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added "nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, changed "ns_type" value from grid to simple, changed "rcoulomb" and "rvdw" values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one. http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. Why are you employing the free energy code? It seems to me this could be the source of your problems. Each molecule alone is fine, but then by decoupling van der Waals and Coulombic interactions between them, you could be getting instability. Turn off the free energy options and see if you get stable trajectories. -Justin Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dna and cnt get distorted in md simulation
Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added "nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, changed "ns_type" value from grid to simple, changed "rcoulomb" and "rvdw" values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. Thanks, Majid-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
