Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 6/6/18 11:13 AM, Eisenhart, Andrew (eisenhaw) wrote: new link with sole mdp file https://files.fm/u/cmyg863c This system doesn't even survive energy minimization for me, suggesting that the topology is not stable. The machine I'm on uses GROMACS 2016.3. Please upgrade to at least that version, if not 2018.1, because 5.1.2 is not even the terminal version in that series. Your topology specifies a SETTLE geometry for an SPC-like water, which immediately leads to each of your waters (which have O-H distances of 0.181 nm and H-H of 0.286 nm) to shrink inward, also shifting your virtual sites. That minimization simply crashes. I changed the SETTLE geometry to agree with your initial geometry, and while the atomic sites are OK, the qh1 and qh2 virtual sites expand outward, and though EM finishes, the max force is on the order of 10^8. Check your virtual site construction, as this may be the source of the buildup in force. Use "nstxout = 1" in your em.mdp to see this happening more clearly. Your cutoffs are bizarrely short but don't seem to be a problem. Once you've sorted out your topology issues, make sure your physical model is sane with such tiny cutoffs. -Justin From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 9:30 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote: Sorry about that, he’s a another link to the same files with the fixed em.mdp. I hope the 7zip format is ok. Please use tgz or just upload a plain-text em.mdp. -Justin https://files.fm/u/r65e3kzq [https://files.fm/images/files.fm-fb.png]<https://files.fm/u/r65e3kzq> 2018-06-06_r65e3kzq<https://files.fm/u/r65e3kzq> files.fm Fast, Secure and Easy cloud file hosting, storage and safe sharing. FTP alternative. Free signup. Unlimited download traffic via torrents. Andrew E. Eisenhart Graduate Research Assistant | University of Cincinnati 330.383.5061 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 7:05:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. em.mdp is some corrupted binary file. Please upload a corrected version. -Justin <https://files.fm/u/c9uef9qh> https://files.fm/u/c9uef9qh Thanks Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 12:54:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation
Re: [gmx-users] Virtual sites causing npt simulation instabilities
new link with sole mdp file https://files.fm/u/cmyg863c From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 9:30 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote: > Sorry about that, he’s a another link to the same files with the fixed > em.mdp. I hope the 7zip format is ok. Please use tgz or just upload a plain-text em.mdp. -Justin > https://files.fm/u/r65e3kzq [https://files.fm/images/files.fm-fb.png]<https://files.fm/u/r65e3kzq> 2018-06-06_r65e3kzq<https://files.fm/u/r65e3kzq> files.fm Fast, Secure and Easy cloud file hosting, storage and safe sharing. FTP alternative. Free signup. Unlimited download traffic via torrents. > > Andrew E. Eisenhart > Graduate Research Assistant | University of Cincinnati > 330.383.5061 > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Justin > Lemkul > Sent: Tuesday, June 5, 2018 7:05:51 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities > > > > On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: >> Here's the link to the files, if there's anything else I can send let me >> know. I've been using 5.1.1 for the initial set up and energy minimization, >> and 5.1.2 for the nvt and npt simulations. >> > em.mdp is some corrupted binary file. Please upload a corrected version. > > -Justin > >> <https://files.fm/u/c9uef9qh> >> >> https://files.fm/u/c9uef9qh >> >> >> >> Thanks >> >> Andrew >> >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> on behalf of Justin >> Lemkul >> Sent: Tuesday, June 5, 2018 12:54:50 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities >> >> >> >> On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: >>> Hello again, >>> >>> I have done a few things since I last updated this list. >>> >>> >>> I generated a new system of only 1000 water instead of the original 2000, I >>> used a more careful approach in my energy minimization, minimizing first >>> with all bonds and angles constrained then again without those hash >>> constraints. This succeeded in getting the maximum force in my system to >>> below 100kcal without lincs warnings. >>> >>> >>> Then I proceeded to equilibrate the temperature as before with no issues, >>> and finally I attempted to equilibrate the box size using the Berendsen >>> barostat running for 2ns. The box size increases as before and still does >>> not converge. The system stays at around 300K, but after a while (~1ns) it >>> seems to fill the box like its a gas visually at least. >>> >>> So any ideas that I could try would be appreciated. >> If you can assemble a tarball that contains starting coordinates (not >> minimized), topology, all .mdp files, and a run script that gives the >> exact sequence of what you're doing, and post it somewhere to share, I >> will try to take a look at it and see if I can reproduce the behavior. >> >> What version of GROMACS are you using? >> >> -Justin >> >>> Thanks, >>> >>> Andrew >>> >>> >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >>> on behalf of Eisenhart, >>> Andrew (eisenhaw) >>> Sent: Thursday, May 31, 2018 1:51:51 PM >>> To: gmx-us...@gromacs.org >>> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities >>> >>> Hey, >>> >>> Thanks for everyone's response. >>> >>> >>> I have tried using the berendsen barostat, with it I see similar behavior >>> with the unit cell jumping up in size and then steadily increasing in size. >>> I have some longer runs using it running now (2-3ns), so I'll be able to >>> see it it eventually converges. >>> >>> >>> Nice catch with the particle type being incorrect, but with it corrected >>> I'm still having the same problems (ie the oscillation of the box size) it >>> has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to >>> simulate for a longer amount of time to see if it will converge. >>> >>> >>
Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote: Sorry about that, he’s a another link to the same files with the fixed em.mdp. I hope the 7zip format is ok. Please use tgz or just upload a plain-text em.mdp. -Justin https://files.fm/u/r65e3kzq Andrew E. Eisenhart Graduate Research Assistant | University of Cincinnati 330.383.5061 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 7:05:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. em.mdp is some corrupted binary file. Please upload a corrected version. -Justin <https://files.fm/u/c9uef9qh> https://files.fm/u/c9uef9qh Thanks Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 12:54:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Sorry about that, he’s a another link to the same files with the fixed em.mdp. I hope the 7zip format is ok. https://files.fm/u/r65e3kzq Andrew E. Eisenhart Graduate Research Assistant | University of Cincinnati 330.383.5061 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 7:05:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: > Here's the link to the files, if there's anything else I can send let me > know. I've been using 5.1.1 for the initial set up and energy minimization, > and 5.1.2 for the nvt and npt simulations. > em.mdp is some corrupted binary file. Please upload a corrected version. -Justin > <https://files.fm/u/c9uef9qh> > > https://files.fm/u/c9uef9qh > > > > Thanks > > Andrew > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Justin > Lemkul > Sent: Tuesday, June 5, 2018 12:54:50 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities > > > > On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: >> Hello again, >> >> I have done a few things since I last updated this list. >> >> >> I generated a new system of only 1000 water instead of the original 2000, I >> used a more careful approach in my energy minimization, minimizing first >> with all bonds and angles constrained then again without those hash >> constraints. This succeeded in getting the maximum force in my system to >> below 100kcal without lincs warnings. >> >> >> Then I proceeded to equilibrate the temperature as before with no issues, >> and finally I attempted to equilibrate the box size using the Berendsen >> barostat running for 2ns. The box size increases as before and still does >> not converge. The system stays at around 300K, but after a while (~1ns) it >> seems to fill the box like its a gas visually at least. >> >> So any ideas that I could try would be appreciated. > If you can assemble a tarball that contains starting coordinates (not > minimized), topology, all .mdp files, and a run script that gives the > exact sequence of what you're doing, and post it somewhere to share, I > will try to take a look at it and see if I can reproduce the behavior. > > What version of GROMACS are you using? > > -Justin > >> Thanks, >> >> Andrew >> >> ________________ >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> on behalf of Eisenhart, >> Andrew (eisenhaw) >> Sent: Thursday, May 31, 2018 1:51:51 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities >> >> Hey, >> >> Thanks for everyone's response. >> >> >> I have tried using the berendsen barostat, with it I see similar behavior >> with the unit cell jumping up in size and then steadily increasing in size. >> I have some longer runs using it running now (2-3ns), so I'll be able to see >> it it eventually converges. >> >> >> Nice catch with the particle type being incorrect, but with it corrected I'm >> still having the same problems (ie the oscillation of the box size) it has >> yet to throw lincs warnings though (even at ts = 2fs) so I'm going to >> simulate for a longer amount of time to see if it will converge. >> >> >> Thanks again for everyone's reply, below is my .itp in its entirety maybe >> there is an error in the exceptions(which im still not 100% sure about) or >> something else that will stand out. >> >> >> Andrew >> >> >> ; >> >> [ atomtypes ] >> ; name bond_typemasscharge ptype sigma epsilon >> qm1 qm1 0.000 -2.516V 0.000 0.000 >> qh1 qh1 0.0001.258V 0.000 0.000 >> >> [ moleculetype ] >> ; molname nrexcl >> M3 3 >> >> [ atoms ] >> ; idat type res nr residu name at name cg nr charge >> 1 opls_1131 M3 OW 1 0.0 >> 2 opls_1141 M3 HW1 1 0.0 >> 3 opls_1141 M3 HW2 1 0.0 >> 4 qm1 1 M3 qm 1 -2.516 >> 5 qh1 1 M3 qh1 1 1.258 >> 6 qh1 1 M3 qh2 1 1.258 &
Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. em.mdp is some corrupted binary file. Please upload a corrected version. -Justin <https://files.fm/u/c9uef9qh> https://files.fm/u/c9uef9qh Thanks Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 12:54:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Thursday, May 31, 2018 7:54:09 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: Hello all, I am having an issue with the current system
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. <https://files.fm/u/c9uef9qh> https://files.fm/u/c9uef9qh Thanks Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 12:54:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: > Hello again, > > I have done a few things since I last updated this list. > > > I generated a new system of only 1000 water instead of the original 2000, I > used a more careful approach in my energy minimization, minimizing first with > all bonds and angles constrained then again without those hash constraints. > This succeeded in getting the maximum force in my system to below 100kcal > without lincs warnings. > > > Then I proceeded to equilibrate the temperature as before with no issues, and > finally I attempted to equilibrate the box size using the Berendsen barostat > running for 2ns. The box size increases as before and still does not > converge. The system stays at around 300K, but after a while (~1ns) it seems > to fill the box like its a gas visually at least. > > So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin > Thanks, > > Andrew > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Eisenhart, > Andrew (eisenhaw) > Sent: Thursday, May 31, 2018 1:51:51 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities > > Hey, > > Thanks for everyone's response. > > > I have tried using the berendsen barostat, with it I see similar behavior > with the unit cell jumping up in size and then steadily increasing in size. I > have some longer runs using it running now (2-3ns), so I'll be able to see it > it eventually converges. > > > Nice catch with the particle type being incorrect, but with it corrected I'm > still having the same problems (ie the oscillation of the box size) it has > yet to throw lincs warnings though (even at ts = 2fs) so I'm going to > simulate for a longer amount of time to see if it will converge. > > > Thanks again for everyone's reply, below is my .itp in its entirety maybe > there is an error in the exceptions(which im still not 100% sure about) or > something else that will stand out. > > > Andrew > > > ; > > [ atomtypes ] > ; name bond_typemasscharge ptype sigma epsilon >qm1 qm1 0.000 -2.516V 0.000 0.000 >qh1 qh1 0.0001.258V 0.000 0.000 > > [ moleculetype ] > ; molname nrexcl > M3 3 > > [ atoms ] > ; idat type res nr residu name at name cg nr charge > 1 opls_1131 M3 OW 1 0.0 > 2 opls_1141 M3 HW1 1 0.0 > 3 opls_1141 M3 HW2 1 0.0 > 4 qm1 1 M3 qm 1 -2.516 > 5 qh1 1 M3 qh1 1 1.258 > 6 qh1 1 M3 qh2 1 1.258 > #ifndef FLEXIBLE > > [ settles ] > ; OWfunct dohdhh > 1 1 0.095720.15139 > #else > [ bonds ] > ; i j funct length force.c. > 1 2 1 0.09572 502416.0 0.09572502416.0 > 1 3 1 0.09572 502416.0 0.09572502416.0 > > [ angles ] > ; i j k funct angle force.c. > 2 1 3 1 104.52 628.02 104.52 628.02 > #endif > > [ exclusions ] > 1 2 3 4 5 6 > 2 1 3 4 5 6 > 3 1 2 4 5 6 > 4 1 2 3 5 6 > 5 1 2 3 4 6 > 6 1 2 3 4 5 > > [ virtual_sites3 ] > ; Vsite fromfunct a b > 4 1 2 3 1 0.29869481802 0.29869481802 > ; Vsite (3fad) funct theta d > 5 3 2 1 3 18.060.025 > 6 2 3 1 3 18.060.025 > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Mark Abraham > > Sent: Thursday, May 31, 2018 7:54:09 AM > To: gmx-us...@gromacs.org > Sub
Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Thursday, May 31, 2018 7:54:09 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: Hello all, I am having an issue with the current systems I am working on. The system consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and hw2; and 3 massless point charges for the electrostatics). The three point charges I have implemented as virtual interaction sites using the section below in my topology file. [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 this is loosely based on the tip4p model. Since the two partial charges off of the hydrogens differ only in location I have them defined as a single type with sigma
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Thursday, May 31, 2018 7:54:09 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: > > > On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: > > Hello all, > > > > I am having an issue with the current systems I am working on. The > system consists of 2000 6point water molecules (3 chargeless masses for Ow, > hw1, and hw2; and 3 massless point charges for the electrostatics). The > three point charges I have implemented as virtual interaction sites using > the section below in my topology file. > > > > > > [ virtual_sites3 ] > > ; Vsite fromfunct a b > > 4 1 2 3 1 0.29869481802 0.29869481802 > > ; Vsite (3fad) functtheta d > > 5 3 2 1 3 18.060.025 > > 6 2 3 1 3 18.060.025 > > > > > > this is loosely based on the tip4p model. Since the two partial charges > off of the hydrogens differ only in location I have them defined as a > single type with sigma and epsilon defined as 0. I have also done this to > the partial charge off of the oxygen. This is all seen below in my > atomtypes and atoms sections. > > > > > > [ atomtypes ] > > ; nam
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Thursday, May 31, 2018 7:54:09 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: > > > On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: > > Hello all, > > > > I am having an issue with the current systems I am working on. The > system consists of 2000 6point water molecules (3 chargeless masses for Ow, > hw1, and hw2; and 3 massless point charges for the electrostatics). The > three point charges I have implemented as virtual interaction sites using > the section below in my topology file. > > > > > > [ virtual_sites3 ] > > ; Vsite fromfunct a b > > 4 1 2 3 1 0.29869481802 0.29869481802 > > ; Vsite (3fad) functtheta d > > 5 3 2 1 3 18.060.025 > > 6 2 3 1 3 18.060.025 > > > > > > this is loosely based on the tip4p model. Since the two partial charges > off of the hydrogens differ only in location I have them defined as a > single type with sigma and epsilon defined as 0. I have also done this to > the partial charge off of the oxygen. This is all seen below in my > atomtypes and atoms sections. > > > > > > [ atomtypes ] > > ; name bond_typemasscharge ptype sigma epsilon > >qm1 qm1 0.000 -2.516A 0.000 0.000 > >qh1 qh1 0.0001.258A 0.000 0.000 > > The particle type for these should be V. This could be the problem - if > you've encoded an incorrect particle type then the update routines will > not propagate them correctly. > > -Justin > > > --- > > > > [ atoms ] > > ; idat type res nr residu name at name cg nr charge > > 1 opls_1131 M3 OW 1 0.0 > > 2 opls_1141 M3 HW1 1 0.0 > > 3 opls_1141 M3 HW2 1 0.0 > > 4 qm1 1 M3 qm 1 -2.516 > > 5 qh1 1 M3 qh1 1 1.258 > > 6 qh1 1 M3 qh2 1 1.258 > > > > The problem I am seeing right now depends on the parameters I use in the > mdp files. D
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: > > > On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: > > Hello all, > > > > I am having an issue with the current systems I am working on. The > system consists of 2000 6point water molecules (3 chargeless masses for Ow, > hw1, and hw2; and 3 massless point charges for the electrostatics). The > three point charges I have implemented as virtual interaction sites using > the section below in my topology file. > > > > > > [ virtual_sites3 ] > > ; Vsite fromfunct a b > > 4 1 2 3 1 0.29869481802 0.29869481802 > > ; Vsite (3fad) functtheta d > > 5 3 2 1 3 18.060.025 > > 6 2 3 1 3 18.060.025 > > > > > > this is loosely based on the tip4p model. Since the two partial charges > off of the hydrogens differ only in location I have them defined as a > single type with sigma and epsilon defined as 0. I have also done this to > the partial charge off of the oxygen. This is all seen below in my > atomtypes and atoms sections. > > > > > > [ atomtypes ] > > ; name bond_typemasscharge ptype sigma epsilon > >qm1 qm1 0.000 -2.516A 0.000 0.000 > >qh1 qh1 0.0001.258A 0.000 0.000 > > The particle type for these should be V. This could be the problem - if > you've encoded an incorrect particle type then the update routines will > not propagate them correctly. > > -Justin > > > --- > > > > [ atoms ] > > ; idat type res nr residu name at name cg nr charge > > 1 opls_1131 M3 OW 1 0.0 > > 2 opls_1141 M3 HW1 1 0.0 > > 3 opls_1141 M3 HW2 1 0.0 > > 4 qm1 1 M3 qm 1 -2.516 > > 5 qh1 1 M3 qh1 1 1.258 > > 6 qh1 1 M3 qh2 1 1.258 > > > > The problem I am seeing right now depends on the parameters I use in the > mdp files. During thermostat equlibration nothing is amiss, but once the > volume of the box is allowed to relax the problems show. Using the > parrinello-rahman barostat and 0.002fs timestep I crash with lincs > warnings. Reducing the timestep to 0.001fs stops the lincs warnings, but > the box size never converges It instead expands to around 10x its original > size. So I think that I must have a problem with the implementation of my > virtual sites. Any guidance would be greatly appreciated. Thanks below are > some other parameters I have set in my input files. > > > > Andrew > > > > > > integrator = md > > nsteps = 50 > > nstcomm = 100 > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > nstlog = 1000 > > nstenergy = 1000 > > nstxtcout = 1000 > > nstlist = 5 > > ns_type = grid > > pbc = xyz > > coulombtype = pme > > rcoulomb= 0.5 > > rlist = 0.5 > > vdw-type= cut-off > > rvdw=0.5 > > constraint_algorithm = lincs > > constraints = all-bonds > > lincs_iter = 1 > > lincs_order = 8 > > fourierspacing = 0.10 > > pme_order= 6 > > ewald_rtol = 1e-06 > > ewald_geometry = 3d > > optimize_fft = yes > > tcoupl = Nose-Hoover > > tc-grps = System > > tau_t = 0.4 > > ref_t = 300 > > ; Pressure coupling is on > > pcoupl = parrinello-rahman > > pcoupltype = isotropic > > tau_p = 2.0 > > ref_p = 1.0 > > compressibility = 4.5e-5 > > refcoord-scaling = com > > DispCorr= EnerPres > > comm-mode = linear > > > > > > > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: Hello all, I am having an issue with the current systems I am working on. The system consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and hw2; and 3 massless point charges for the electrostatics). The three point charges I have implemented as virtual interaction sites using the section below in my topology file. [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 this is loosely based on the tip4p model. Since the two partial charges off of the hydrogens differ only in location I have them defined as a single type with sigma and epsilon defined as 0. I have also done this to the partial charge off of the oxygen. This is all seen below in my atomtypes and atoms sections. [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516A 0.000 0.000 qh1 qh1 0.0001.258A 0.000 0.000 The particle type for these should be V. This could be the problem - if you've encoded an incorrect particle type then the update routines will not propagate them correctly. -Justin --- [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 The problem I am seeing right now depends on the parameters I use in the mdp files. During thermostat equlibration nothing is amiss, but once the volume of the box is allowed to relax the problems show. Using the parrinello-rahman barostat and 0.002fs timestep I crash with lincs warnings. Reducing the timestep to 0.001fs stops the lincs warnings, but the box size never converges It instead expands to around 10x its original size. So I think that I must have a problem with the implementation of my virtual sites. Any guidance would be greatly appreciated. Thanks below are some other parameters I have set in my input files. Andrew integrator = md nsteps = 50 nstcomm = 100 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 nstlist = 5 ns_type = grid pbc = xyz coulombtype = pme rcoulomb= 0.5 rlist = 0.5 vdw-type= cut-off rvdw=0.5 constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 8 fourierspacing = 0.10 pme_order= 6 ewald_rtol = 1e-06 ewald_geometry = 3d optimize_fft = yes tcoupl = Nose-Hoover tc-grps = System tau_t = 0.4 ref_t = 300 ; Pressure coupling is on pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 refcoord-scaling = com DispCorr= EnerPres comm-mode = linear -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Always good practice to use Berendsen when turning on constant pressure first, it is much more robust than P-R. Let that run for awhile, let it equilibrate, then turn on P-R. 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 31 May 2018 at 06:40, Eisenhart, Andrew (eisenhaw) wrote: > Hello all, > > I am having an issue with the current systems I am working on. The system > consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and > hw2; and 3 massless point charges for the electrostatics). The three point > charges I have implemented as virtual interaction sites using the section > below in my topology file. > > > [ virtual_sites3 ] > ; Vsite fromfunct a b > 4 1 2 3 1 0.29869481802 0.29869481802 > ; Vsite (3fad) functtheta d > 5 3 2 1 3 18.060.025 > 6 2 3 1 3 18.060.025 > > > this is loosely based on the tip4p model. Since the two partial charges off > of the hydrogens differ only in location I have them defined as a single type > with sigma and epsilon defined as 0. I have also done this to the partial > charge off of the oxygen. This is all seen below in my atomtypes and atoms > sections. > > > [ atomtypes ] > ; name bond_typemasscharge ptype sigma epsilon > qm1 qm1 0.000 -2.516A 0.000 0.000 > qh1 qh1 0.0001.258A 0.000 0.000 > > --- > > [ atoms ] > ; idat type res nr residu name at name cg nr charge > 1 opls_1131 M3 OW 1 0.0 > 2 opls_1141 M3 HW1 1 0.0 > 3 opls_1141 M3 HW2 1 0.0 > 4 qm1 1 M3 qm 1 -2.516 > 5 qh1 1 M3 qh1 1 1.258 > 6 qh1 1 M3 qh2 1 1.258 > > The problem I am seeing right now depends on the parameters I use in the mdp > files. During thermostat equlibration nothing is amiss, but once the volume > of the box is allowed to relax the problems show. Using the parrinello-rahman > barostat and 0.002fs timestep I crash with lincs warnings. Reducing the > timestep to 0.001fs stops the lincs warnings, but the box size never > converges It instead expands to around 10x its original size. So I think > that I must have a problem with the implementation of my virtual sites. Any > guidance would be greatly appreciated. Thanks below are some other parameters > I have set in my input files. > > Andrew > > > integrator = md > nsteps = 50 > nstcomm = 100 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 1000 > nstenergy = 1000 > nstxtcout = 1000 > nstlist = 5 > ns_type = grid > pbc = xyz > coulombtype = pme > rcoulomb= 0.5 > rlist = 0.5 > vdw-type= cut-off > rvdw=0.5 > constraint_algorithm = lincs > constraints = all-bonds > lincs_iter = 1 > lincs_order = 8 > fourierspacing = 0.10 > pme_order= 6 > ewald_rtol = 1e-06 > ewald_geometry = 3d > optimize_fft = yes > tcoupl = Nose-Hoover > tc-grps = System > tau_t = 0.4 > ref_t = 300 > ; Pressure coupling is on > pcoupl = parrinello-rahman > pcoupltype = isotropic > tau_p = 2.0 > ref_p = 1.0 > compressibility = 4.5e-5 > refcoord-scaling = com > DispCorr= EnerPres > comm-mode = linear > > > > -- > 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] Virtual sites causing npt simulation instabilities
Hello all, I am having an issue with the current systems I am working on. The system consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and hw2; and 3 massless point charges for the electrostatics). The three point charges I have implemented as virtual interaction sites using the section below in my topology file. [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 this is loosely based on the tip4p model. Since the two partial charges off of the hydrogens differ only in location I have them defined as a single type with sigma and epsilon defined as 0. I have also done this to the partial charge off of the oxygen. This is all seen below in my atomtypes and atoms sections. [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516A 0.000 0.000 qh1 qh1 0.0001.258A 0.000 0.000 --- [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 The problem I am seeing right now depends on the parameters I use in the mdp files. During thermostat equlibration nothing is amiss, but once the volume of the box is allowed to relax the problems show. Using the parrinello-rahman barostat and 0.002fs timestep I crash with lincs warnings. Reducing the timestep to 0.001fs stops the lincs warnings, but the box size never converges It instead expands to around 10x its original size. So I think that I must have a problem with the implementation of my virtual sites. Any guidance would be greatly appreciated. Thanks below are some other parameters I have set in my input files. Andrew integrator = md nsteps = 50 nstcomm = 100 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 nstlist = 5 ns_type = grid pbc = xyz coulombtype = pme rcoulomb= 0.5 rlist = 0.5 vdw-type= cut-off rvdw=0.5 constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 8 fourierspacing = 0.10 pme_order= 6 ewald_rtol = 1e-06 ewald_geometry = 3d optimize_fft = yes tcoupl = Nose-Hoover tc-grps = System tau_t = 0.4 ref_t = 300 ; Pressure coupling is on pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 refcoord-scaling = com DispCorr= EnerPres comm-mode = linear -- 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.
