Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi Chris, I actually use the mdp file suggested by CHARMM-GUI. I figured they had tested this set-up extensively. Regarding the wacky init pdb, it has indeed been previously equilibrated using the Berendsen barostat for 20 ns, however, I will now run, as you suggest, a much longer equilibration

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

On 10/31/18 12:39 PM, Chris Neale wrote: First, your init.pdb is really wacky. You've got a bleb in the membrane. That appears to heal rapidly during simulation, but the Z-axis fluctuations look pretty large to me. I suspect you're running into a known problem with P-R pressure coupling,

[gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

First, your init.pdb is really wacky. You've got a bleb in the membrane. That appears to heal rapidly during simulation, but the Z-axis fluctuations look pretty large to me. I suspect you're running into a known problem with P-R pressure coupling, which is that oscillations can get out of hand if

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

On 10/31/18 11:06 AM, Ramon Guixà wrote: Ok, I mean, It makes sense what you say. I still I don't understand though how this has not been spotted before, I mean, I presume this combination is widely used (CHARMM+GROMACS+GPUs) and I have replicated the problem using versions 5, 2016, and

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Ok, I mean, It makes sense what you say. I still I don't understand though how this has not been spotted before, I mean, I presume this combination is widely used (CHARMM+GROMACS+GPUs) and I have replicated the problem using versions 5, 2016, and 2018...? I know I sound a little desperate, but is

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

On 10/31/18 10:47 AM, Ramon Guixà wrote: Hi Justin, I do not have access to GPUs with ECC, but I have actually run the same tpr in different machines with different GPUs, including GTX 980, 1060 and 1080. In all cases, I get the same problem. Although they are all non-ECC cards, it is quite

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi Justin, I do not have access to GPUs with ECC, but I have actually run the same tpr in different machines with different GPUs, including GTX 980, 1060 and 1080. In all cases, I get the same problem. Although they are all non-ECC cards, it is quite unlikely that a bit flip is behind this,

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

On 10/31/18 8:36 AM, Ramon Guixà wrote: Hi again, Just confirmed that when I run the same tpr file for 500 ns using only CPUs, no problems arise, please check it out here: https://drive.google.com/open?id=1aI2wr2GvNjCfj4c4J0pmgCzV0ak5FRE6

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi again, Just confirmed that when I run the same tpr file for 500 ns using only CPUs, no problems arise, please check it out here: https://drive.google.com/open?id=1aI2wr2GvNjCfj4c4J0pmgCzV0ak5FRE6 I mean, is this a bug? Most

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi Kevin, I already changed all to h-bonds with no effect at all, but thanks for pointing it out anyway. Please download log and edr files from this link below: https://drive.google.com/open?id=12DezJ9DEijlE1VKbWnu4-WDzHMqDpnKx Ramon On Tue, Oct 30, 2018 at 7:57 PM Kevin Boyd wrote: > Hi, > >

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi, Can you send an edr and log file? I believe your constraints are nonstandard, iirc for charmm36 constraints should just be h-bonds, but I doubt that would cause this. Kevin On Tue, Oct 30, 2018 at 2:50 PM, Ramon Guixà wrote: > Hi Mark, thanks for the quick response > > No transition

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi Mark, thanks for the quick response No transition expected, just pure POPC at 310K. In any case, I never saw such box fluctuations during production before... Any hint? R On Tue, 30 Oct 2018, 19:41 Mark Abraham, wrote: > Hi, > > Your end point is a wildly different lipid configuration. Is

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi, Your end point is a wildly different lipid configuration. Is such a (phase?) transition expected? Mark On Tue, Oct 30, 2018 at 7:24 PM Ramon Guixà wrote: > Dear all, > > After several years simulating membrane proteins using GROMACS and the > CHARMM force field, I have come across this

[gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Dear all, After several years simulating membrane proteins using GROMACS and the CHARMM force field, I have come across this issue: I use the CHARMM-GUI interface to prepare my membrane-protein system, that I subsequently equilibrate using a standard protocol. However, after several ns, namely