Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2
On 10/20/16 9:39 AM, Chapman, Christopher W. wrote: Hi, Thank you for your helpful comments and suggestions. Per your recommendations, I tried running my simulation with the original parameter set and configuration file, and the forces behave as one would expect. I tried re-generating the configuration file, however, and the simulation breaks down. I apparently created a correct configuration file once, and cannot recreate it. From what I can tell, since I'm using the TIP4P/2005f model, I cannot use Gromacs' built in solvate command because the .gro file it calls is based on the TIP4P model, which has slightly different values for the bond lengths and angles (though I may be wrong about not being able to use solvate). Because of this, I used my aforementioned script and just set the parameter values to their defaults given by the TIP4P/2005f model. The script generates the configuration file by creating an individual water molecule, randomly rotating it, and placing it in the box. This process is repeated until the box is full. Each molecule is offset from each other molecule by a set amount so that there is no overlap between any two water molecules. Each molecule is also checked to confirm that the rotations didn't alter the bond lengths, bond angles, and to ensure that all of the atoms lie in the same plane (there's no reason why the rotation should change these, but I figured I'd check just t o be safe). Is this an appropriate way to create the configuration file 'by hand'? Just use the existing tip4p.gro and minimize it using the new topology. Then you'll know immediately if the new topology is sensible, without complications of possible bad configurations. -Justin Thanks, Chris -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, October 18, 2016 18:46 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2 On 10/18/16 12:20 PM, Chapman, Christopher W. wrote: Hi Mark, Yes, my implementation does work for standard parameter values. I agree with Mark. You likely have a bad parameter set, and mdrun is telling you it is crashing. Compute the forces in that trajectory and likely you will see where some bad behavior is emerging. Force fields can be delicate, so what may seem like some small change can actually have profound consequences for stability. -Justin Thanks, Chris -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Tuesday, October 18, 2016 11:55 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2 Hi, This looks like one manifestation of "the model physics is broken, and so is the resulting simulation system." Does your implementation behave for standard parameter values? Mark On Tue, Oct 18, 2016 at 5:34 PM Chapman, Christopher W. wrote: Hello all, I am trying to model TIP4P/2005f water using Gromacs 5.1.2. Specifically, I'm trying to show how modifying the parameters of the TIP4P/2005f model changes the density of states. I wrote a small script to randomly vary the parameters and write out the .gro and .top files. When I tried running my molecular dynamics run, however, I got the following message: A list of missing interactions: Morse of686 missing 1 Molecule type 'WAT' the first 10 missing interactions, except for exclusions: Morse atoms13 global6971 Fatal error: 1 of the 1029 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.294303 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website I'm trying to figure out if this error is because the random values for the parameters I chose were bad values (I sample them from a log-normal distribution with a mean of the defined values of the TIP4P/2005f values and a variance of 1% of those values), or if my script is writing out the .gro and .top files incorrectly, or some other cause. Any help that could be provided would be greatly appreciated. Thank you, Chris -- 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 arc
Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2
Hi, Thank you for your helpful comments and suggestions. Per your recommendations, I tried running my simulation with the original parameter set and configuration file, and the forces behave as one would expect. I tried re-generating the configuration file, however, and the simulation breaks down. I apparently created a correct configuration file once, and cannot recreate it. >From what I can tell, since I'm using the TIP4P/2005f model, I cannot use >Gromacs' built in solvate command because the .gro file it calls is based on >the TIP4P model, which has slightly different values for the bond lengths and >angles (though I may be wrong about not being able to use solvate). Because of >this, I used my aforementioned script and just set the parameter values to >their defaults given by the TIP4P/2005f model. The script generates the >configuration file by creating an individual water molecule, randomly rotating >it, and placing it in the box. This process is repeated until the box is full. >Each molecule is offset from each other molecule by a set amount so that there >is no overlap between any two water molecules. Each molecule is also checked >to confirm that the rotations didn't alter the bond lengths, bond angles, and >to ensure that all of the atoms lie in the same plane (there's no reason why >the rotation should change these, but I figured I'd check just to be safe). Is this an appropriate way to create the configuration file 'by hand'? Thanks, Chris -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, October 18, 2016 18:46 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2 On 10/18/16 12:20 PM, Chapman, Christopher W. wrote: > Hi Mark, > > Yes, my implementation does work for standard parameter values. > I agree with Mark. You likely have a bad parameter set, and mdrun is telling you it is crashing. Compute the forces in that trajectory and likely you will see where some bad behavior is emerging. Force fields can be delicate, so what may seem like some small change can actually have profound consequences for stability. -Justin > Thanks, > > Chris > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf > Of Mark Abraham > Sent: Tuesday, October 18, 2016 11:55 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs > 5.1.2 > > Hi, > > This looks like one manifestation of "the model physics is broken, and so is > the resulting simulation system." Does your implementation behave for > standard parameter values? > > Mark > > On Tue, Oct 18, 2016 at 5:34 PM Chapman, Christopher W. > > wrote: > >> Hello all, >> >> I am trying to model TIP4P/2005f water using Gromacs 5.1.2. >> Specifically, I'm trying to show how modifying the parameters of the >> TIP4P/2005f model changes the density of states. I wrote a small >> script to randomly vary the parameters and write out the .gro and >> .top files. When I tried running my molecular dynamics run, however, I got >> the following message: >> >> >> A list of missing interactions: >>Morse of686 missing 1 >> >> Molecule type 'WAT' >> the first 10 missing interactions, except for exclusions: >>Morse atoms13 global6971 >> >> Fatal error: >> 1 of the 1029 bonded interactions could not be calculated because >> some atoms involved moved further apart than the multi-body cut-off >> distance >> (0.294303 nm) or the two-body cut-off distance (1 nm), see option >> -rdd, for pairs and tabulated bonds also see option -ddcheck For more >> information and tips for troubleshooting, please check the GROMACS >> website >> >> >> I'm trying to figure out if this error is because the random values >> for the parameters I chose were bad values (I sample them from a >> log-normal distribution with a mean of the defined values of the >> TIP4P/2005f values and a variance of 1% of those values), or if my >> script is writing out the .gro and .top files incorrectly, or some >> other cause. Any help that could be provided would be greatly appreciated. >> >> Thank you, >> >> Chris >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_List
Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2
On 10/18/16 12:20 PM, Chapman, Christopher W. wrote: Hi Mark, Yes, my implementation does work for standard parameter values. I agree with Mark. You likely have a bad parameter set, and mdrun is telling you it is crashing. Compute the forces in that trajectory and likely you will see where some bad behavior is emerging. Force fields can be delicate, so what may seem like some small change can actually have profound consequences for stability. -Justin Thanks, Chris -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Tuesday, October 18, 2016 11:55 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2 Hi, This looks like one manifestation of "the model physics is broken, and so is the resulting simulation system." Does your implementation behave for standard parameter values? Mark On Tue, Oct 18, 2016 at 5:34 PM Chapman, Christopher W. wrote: Hello all, I am trying to model TIP4P/2005f water using Gromacs 5.1.2. Specifically, I'm trying to show how modifying the parameters of the TIP4P/2005f model changes the density of states. I wrote a small script to randomly vary the parameters and write out the .gro and .top files. When I tried running my molecular dynamics run, however, I got the following message: A list of missing interactions: Morse of686 missing 1 Molecule type 'WAT' the first 10 missing interactions, except for exclusions: Morse atoms13 global6971 Fatal error: 1 of the 1029 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.294303 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website I'm trying to figure out if this error is because the random values for the parameters I chose were bad values (I sample them from a log-normal distribution with a mean of the defined values of the TIP4P/2005f values and a variance of 1% of those values), or if my script is writing out the .gro and .top files incorrectly, or some other cause. Any help that could be provided would be greatly appreciated. Thank you, Chris -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] TIP4P/2005f parameter modification in Gromacs 5.1.2
Hi Mark, Yes, my implementation does work for standard parameter values. Thanks, Chris -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Tuesday, October 18, 2016 11:55 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2 Hi, This looks like one manifestation of "the model physics is broken, and so is the resulting simulation system." Does your implementation behave for standard parameter values? Mark On Tue, Oct 18, 2016 at 5:34 PM Chapman, Christopher W. wrote: > Hello all, > > I am trying to model TIP4P/2005f water using Gromacs 5.1.2. > Specifically, I'm trying to show how modifying the parameters of the > TIP4P/2005f model changes the density of states. I wrote a small > script to randomly vary the parameters and write out the .gro and .top > files. When I tried running my molecular dynamics run, however, I got the > following message: > > > A list of missing interactions: >Morse of686 missing 1 > > Molecule type 'WAT' > the first 10 missing interactions, except for exclusions: >Morse atoms13 global6971 > > Fatal error: > 1 of the 1029 bonded interactions could not be calculated because some > atoms involved moved further apart than the multi-body cut-off > distance > (0.294303 nm) or the two-body cut-off distance (1 nm), see option > -rdd, for pairs and tabulated bonds also see option -ddcheck For more > information and tips for troubleshooting, please check the GROMACS > website > > > I'm trying to figure out if this error is because the random values > for the parameters I chose were bad values (I sample them from a > log-normal distribution with a mean of the defined values of the > TIP4P/2005f values and a variance of 1% of those values), or if my > script is writing out the .gro and .top files incorrectly, or some > other cause. Any help that could be provided would be greatly appreciated. > > Thank you, > > Chris > > -- > 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] TIP4P/2005f parameter modification in Gromacs 5.1.2
Hi, This looks like one manifestation of "the model physics is broken, and so is the resulting simulation system." Does your implementation behave for standard parameter values? Mark On Tue, Oct 18, 2016 at 5:34 PM Chapman, Christopher W. wrote: > Hello all, > > I am trying to model TIP4P/2005f water using Gromacs 5.1.2. Specifically, > I'm trying to show how modifying the parameters of the TIP4P/2005f model > changes the density of states. I wrote a small script to randomly vary the > parameters and write out the .gro and .top files. When I tried running my > molecular dynamics run, however, I got the following message: > > > A list of missing interactions: >Morse of686 missing 1 > > Molecule type 'WAT' > the first 10 missing interactions, except for exclusions: >Morse atoms13 global6971 > > Fatal error: > 1 of the 1029 bonded interactions could not be calculated because some > atoms involved moved further apart than the multi-body cut-off distance > (0.294303 nm) or the two-body cut-off distance (1 nm), see option -rdd, for > pairs and tabulated bonds also see option -ddcheck > For more information and tips for troubleshooting, please check the > GROMACS website > > > I'm trying to figure out if this error is because the random values for > the parameters I chose were bad values (I sample them from a log-normal > distribution with a mean of the defined values of the TIP4P/2005f values > and a variance of 1% of those values), or if my script is writing out the > .gro and .top files incorrectly, or some other cause. Any help that could > be provided would be greatly appreciated. > > Thank you, > > Chris > > -- > 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.
