[gmx-users] COM coordinate fix
Dear all, We have 80 polymers in the simulation box, for some reason, we want to make the COM of each polymer be fixed. Is this possible in Gromacs with any command, or somewhere in the source code we can change the expression of displacement along with time . Thank you very much in advance. Kind regards, Li -- 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] mdrun WARING and crash
Hallo Justin, Thank you for your reply, I uploaded the images, Please find following the link below, start box: http://s1279.beta.photobucket.com/user/Li_Liu/media/image0_zpsf95d10fe.jpeg.html?filters[user]=134822327filters[recent]=1filters[publicOnly]=1sort=1o=1 and snapshot for first step: http://s1279.beta.photobucket.com/user/Li_Liu/media/image1_zps06f589e6.jpeg.html?filters[user]=134822327filters[recent]=1filters[publicOnly]=1sort=1o=0 Thanks a lot, and have a nice day. Kind regards, Li From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Monday, March 11, 2013 10:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On Monday, March 11, 2013, wrote: Hallo Justin, Thank you for your comments. Taking your suggestions, I set nrexcl=1, and comment the [pairs] section, because there is no special case of non-bonded interactions to declare, then we try to see what happens. Now we minimize it by steep, then by cg, both of the processor are very quick done, because after around 7000 steps, the energy can not go further down any more. Then we finish the mdrun, the energies output are like: Step Time Lambda 1 10.00.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 1.49468e+050.0e+001.49468e+058.73890e+031.58207e+05 Temperature Pressure (bar) 4.38208e+029.93028e+04 Although this time no running error, we find the outputs are extremely wired, for example through VMD conf.gro traj.xtc we find 0 frame a homogeneous box, starting from the first step, the box becomes a lattice, which is far away from our expected the Polymer melt system should be. The force parameters are taken from literature PRL 85(5), 1128(2000), I am still very worried about the format of my input files. Could you please give me, a very beginner a help. Please provide links to images. This is probably not a big deal as long as the simulation is actually running, since a triclinic representation of the unit cell is used. -Justin Thanks a lot. Kind regards, Li From: gmx-users-boun...@gromacs.org javascript:; [ gmx-users-boun...@gromacs.org javascript:;] on behalf of Justin Lemkul [ jalem...@vt.edu javascript:;] Sent: Thursday, February 28, 2013 3:02 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On 2/28/13 6:59 AM, l@utwente.nl wrote: Hallo Justin, Thank you for you help. I have read the previous discussions on this topic, which is very helpful. The link is: http://gromacs.5086.n6.nabble.com/What-is-the-purpose-of-the-pairs-section-td5003598.html Well, there are still something I want to make sure, which might be the reason of mdrun crash of my system. ###Introduction of system## Linear Polyethylene melt: each chain contains 16 beads, each bead coarse grained 3 monomers. Number of chain in the box is 64. Force Field## ffbonded.itp [ bondtypes ] ; FENE, Ro = 1.5 sigma and kb = 30 epsilon/sigma^2 ; ij funcb0 (nm) kb (kJ/mol nm^2) CH2 CH27 0.795 393. ffnonbonded.itp [ atomtypes ] ; epsilon / kB = 443K ;name at.num mass (au) charge ptype sigma (nm) epsilon (kJ/mol) CH2 142.3 0.000 A 0.5300 3.68133 [ nonbond_params ] ; i jfunc sigma epsilon CH2 CH210.5303.68133 [ pairtypes ] ; i jfunc sigma epsilon CH2 CH21 0.533.68133 topology## [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2no 1.0 1.0 ; The force field files to be included #include ../forcefield/forcefield.itp [ moleculetype ] ; name nrexcl PE 0 [atoms] ; nrtype resnr residuatomcgnr charge 1 CH2 1PE C 1 0.0 2 CH2 1PE C 2 0.0 3 CH2 1PE C 3 0.0 4 CH2 1PE C 4 0.0 .. 15CH2 1PE C 15 0.0 16CH2 1PE C 16 0.0 [ bonds ] ; aiaj funct c0 c1 1 2 7 0.795 393. 2 3 7 0.795 393. 3 4 7 0.795 393. .. 1415 7 0.795 393. 1516 7
RE: [gmx-users] mdrun WARING and crash
Hallo Justin, One update on the wired snapshot mentioned on previous email. I checked over the output coordinates and xmgrace it with xy directions, finding that it is not crystal, instead it is a normal homogeneous box. All these give us a clue that it might be the trajectory file goes wrong, cause we calculated the RDF and MSD and view VMD all through traj.xtc. I am checking the way I output the trajectory. Could you please give me your suggestions if there is something wrong on my .mdp file( included in earlier email). It seems that the system now is working, though with still some output errors or perhaps further unexpected problems. Well, so far we got a progress, and I want to say thank you very much for all your help. Kind regards, Li From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Monday, March 11, 2013 10:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On Monday, March 11, 2013, wrote: Hallo Justin, Thank you for your comments. Taking your suggestions, I set nrexcl=1, and comment the [pairs] section, because there is no special case of non-bonded interactions to declare, then we try to see what happens. Now we minimize it by steep, then by cg, both of the processor are very quick done, because after around 7000 steps, the energy can not go further down any more. Then we finish the mdrun, the energies output are like: Step Time Lambda 1 10.00.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 1.49468e+050.0e+001.49468e+058.73890e+031.58207e+05 Temperature Pressure (bar) 4.38208e+029.93028e+04 Although this time no running error, we find the outputs are extremely wired, for example through VMD conf.gro traj.xtc we find 0 frame a homogeneous box, starting from the first step, the box becomes a lattice, which is far away from our expected the Polymer melt system should be. The force parameters are taken from literature PRL 85(5), 1128(2000), I am still very worried about the format of my input files. Could you please give me, a very beginner a help. Please provide links to images. This is probably not a big deal as long as the simulation is actually running, since a triclinic representation of the unit cell is used. -Justin Thanks a lot. Kind regards, Li From: gmx-users-boun...@gromacs.org javascript:; [ gmx-users-boun...@gromacs.org javascript:;] on behalf of Justin Lemkul [ jalem...@vt.edu javascript:;] Sent: Thursday, February 28, 2013 3:02 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On 2/28/13 6:59 AM, l@utwente.nl wrote: Hallo Justin, Thank you for you help. I have read the previous discussions on this topic, which is very helpful. The link is: http://gromacs.5086.n6.nabble.com/What-is-the-purpose-of-the-pairs-section-td5003598.html Well, there are still something I want to make sure, which might be the reason of mdrun crash of my system. ###Introduction of system## Linear Polyethylene melt: each chain contains 16 beads, each bead coarse grained 3 monomers. Number of chain in the box is 64. Force Field## ffbonded.itp [ bondtypes ] ; FENE, Ro = 1.5 sigma and kb = 30 epsilon/sigma^2 ; ij funcb0 (nm) kb (kJ/mol nm^2) CH2 CH27 0.795 393. ffnonbonded.itp [ atomtypes ] ; epsilon / kB = 443K ;name at.num mass (au) charge ptype sigma (nm) epsilon (kJ/mol) CH2 142.3 0.000 A 0.5300 3.68133 [ nonbond_params ] ; i jfunc sigma epsilon CH2 CH210.5303.68133 [ pairtypes ] ; i jfunc sigma epsilon CH2 CH21 0.533.68133 topology## [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2no 1.0 1.0 ; The force field files to be included #include ../forcefield/forcefield.itp [ moleculetype ] ; name nrexcl PE 0 [atoms] ; nrtype resnr residuatomcgnr charge 1 CH2 1PE C 1 0.0 2 CH2 1PE C 2 0.0 3 CH2 1PE C 3 0.0 4 CH2 1PE C 4 0.0 .. 15CH2 1PE C 15 0.0 16CH2 1PE C 16 0.0 [ bonds ] ; aiaj
RE: [gmx-users] mdrun WARING and crash
Hallo Justin, Thank you for your comments. Taking your suggestions, I set nrexcl=1, and comment the [pairs] section, because there is no special case of non-bonded interactions to declare, then we try to see what happens. Now we minimize it by steep, then by cg, both of the processor are very quick done, because after around 7000 steps, the energy can not go further down any more. Then we finish the mdrun, the energies output are like: Step Time Lambda 1 10.00.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 1.49468e+050.0e+001.49468e+058.73890e+031.58207e+05 Temperature Pressure (bar) 4.38208e+029.93028e+04 Although this time no running error, we find the outputs are extremely wired, for example through VMD conf.gro traj.xtc we find 0 frame a homogeneous box, starting from the first step, the box becomes a lattice, which is far away from our expected the Polymer melt system should be. The force parameters are taken from literature PRL 85(5), 1128(2000), I am still very worried about the format of my input files. Could you please give me, a very beginner a help. Thanks a lot. Kind regards, Li From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Thursday, February 28, 2013 3:02 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On 2/28/13 6:59 AM, l@utwente.nl wrote: Hallo Justin, Thank you for you help. I have read the previous discussions on this topic, which is very helpful. The link is: http://gromacs.5086.n6.nabble.com/What-is-the-purpose-of-the-pairs-section-td5003598.html Well, there are still something I want to make sure, which might be the reason of mdrun crash of my system. ###Introduction of system## Linear Polyethylene melt: each chain contains 16 beads, each bead coarse grained 3 monomers. Number of chain in the box is 64. Force Field## ffbonded.itp [ bondtypes ] ; FENE, Ro = 1.5 sigma and kb = 30 epsilon/sigma^2 ; ij funcb0 (nm) kb (kJ/mol nm^2) CH2 CH27 0.795 393. ffnonbonded.itp [ atomtypes ] ; epsilon / kB = 443K ;name at.num mass (au) charge ptype sigma (nm)epsilon (kJ/mol) CH2 142.3 0.000 A 0.5300 3.68133 [ nonbond_params ] ; i jfunc sigma epsilon CH2 CH210.5303.68133 [ pairtypes ] ; i jfunc sigma epsilon CH2 CH21 0.533.68133 topology## [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2no 1.0 1.0 ; The force field files to be included #include ../forcefield/forcefield.itp [ moleculetype ] ; name nrexcl PE 0 [atoms] ; nrtype resnr residuatomcgnr charge 1 CH2 1PE C 1 0.0 2 CH2 1PE C 2 0.0 3 CH2 1PE C 3 0.0 4 CH2 1PE C 4 0.0 .. 15CH2 1PE C 15 0.0 16CH2 1PE C 16 0.0 [ bonds ] ; aiaj funct c0 c1 1 2 7 0.795 393. 2 3 7 0.795 393. 3 4 7 0.795 393. .. 1415 7 0.795 393. 1516 7 0.795 393. [ pairs ] ; aiaj funct c0 c1 1 2 1 0.53 3.68133 1 3 1 0.53 3.68133 1 4 1 0.53 3.68133 2 3 1 0.53 3.68133 2 4 1 0.53 3.68133 2 5 1 0.53 3.68133 .. 1415 1 0.53 3.68133 1416 1 0.53 3.68133 1516 1 0.53 3.68133 ##mdp### ;directories to include in your topology. Format include = -I/home/otterw/Install/gromacs-4.6/src/gmxlib integrator = md ; ; RUN CONTROL * ; tinit = 0; start time to run dt = 1e-3
[gmx-users] question on RDF
Dear all, When calculation the RDF, it asks: Select a reference group and 1 group Group 0 ( System) has 1600 elements Group 1 ( Other) has 1600 elements Group 2 ( PE) has 1600 elements Group 3 ( a_1-1600) has 1600 elements My question is what's the difference between reference group and 1 group, how the RDF calculated for them. Thank you very much. Kind regards, Li -- 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
