Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
What will happen if pbc=full is used? 2008/4/4 maria goranovic [EMAIL PROTECTED]: Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Hi, Sorry for the incomplete details. Here they are now: I started with a well-equilibrated POPC bilayer, and changed one POPC lipid to a lipid of my interest. I wrote the topology file for the new lipid accordingly. After that, I did some simple steepest descent minimization, and followed it up by dynamics. Here is the .mdp file for the runs. There is a preceding 25,000-step simulation where the initial velocities are assigned. The mdp file below is what is being used for equilibrium dynamics. thank you for the suggestions. I will also explore the archives ; ; Input file ; ;- ; BASICS ;- title = dummy-file cpp = /usr/bin/cpp integrator = md tinit = 0 init_step = 25000 nsteps = 10 dt = 0.002 ;- ; BOND PARAMETERS ;- constraints = hbonds constraint_algorithm = lincs unconstrained_start = yes lincs_order = 4 lincs_warnangle = 30 ;- ; OUTPUT CONTROL ;- nstxout = 5000 ; positions nstvout = 5000 ; velocity nstlog = 5000 ; energies to log file nstenergy = 5000 ; energy to energy file ;- ; MISCELLANEOUS ;- comm_mode = linear nstlist = 10 ns_type = grid pbc = xyz ; -- ; NONBONDED INTERACTIONS ; -- coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rlist = 1.0 rvdw= 1.0 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ; --- ; NPT ; --- Tcoupl = berendsen tc-grps = LIP Solvent tau_t = 0.1 0.1 ref_t = 313.0313.0 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.01.0 ; --- gen_vel = no ; --- On Fri, Apr 4, 2008 at 6:44 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Quoting Justin A. Lemkul [EMAIL PROTECTED]: Quoting maria goranovic [EMAIL PROTECTED]: Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. And as an aside, broken bonds are only a visualization effect; mdrun doesn't write broken molecules. Also, providing your .mdp file would be of use. -Justin The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? You'll have to describe how you minimized and equilibrated your bilayer before we'll have any idea what's going on. Also have a thorough look through the archives; many users have posted about bilayers exploding (including yours truly). -Justin Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
maria goranovic wrote: Hi, Sorry for the incomplete details. Here they are now: I started with a well-equilibrated POPC bilayer, and changed one POPC lipid to a lipid of my interest. I wrote the topology file for the new lipid accordingly. This topology change is probably the source of the problem, and would have been a good thing not to describe as a 128-lipid bilayer simulation with standard parameters. After that, I did some simple steepest descent minimization, and followed it up by dynamics. Here is the .mdp file for the runs. There is a preceding 25,000-step simulation where the initial velocities are assigned. The mdp file below is what is being used for equilibrium dynamics. That's all fine. You should have a close look at the structures leading up to the simulation crashes, and pay attention to all of the warning messages from grompp and error messages from mdrun. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Quoting maria goranovic [EMAIL PROTECTED]: Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? You'll have to describe how you minimized and equilibrated your bilayer before we'll have any idea what's going on. Also have a thorough look through the archives; many users have posted about bilayers exploding (including yours truly). -Justin Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Quoting Justin A. Lemkul [EMAIL PROTECTED]: Quoting maria goranovic [EMAIL PROTECTED]: Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. And as an aside, broken bonds are only a visualization effect; mdrun doesn't write broken molecules. Also, providing your .mdp file would be of use. -Justin The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? You'll have to describe how you minimized and equilibrated your bilayer before we'll have any idea what's going on. Also have a thorough look through the archives; many users have posted about bilayers exploding (including yours truly). -Justin Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
