Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Alexander Alexander
On Thursday, April 12, 2018 at 4:55:47 PM UTC-4, Christoph Junghans wrote: > > On Thu, Apr 12, 2018 at 2:28 PM, Alexander Alexander > wrote: > > > > Thank you. > > > > An then these parameter > > 1000 > > 4.0 > > which usually comes in the very end of

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Christoph Junghans
On Thu, Apr 12, 2018 at 2:28 PM, Alexander Alexander wrote: > > Thank you. > > An then these parameter > 1000 > 4.0 > which usually comes in the very end of settings.xml of IBI in the > section, are again mx of potential and end of it, which should be larger > than

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Alexander Alexander
Thank you. An then these parameter 1000 4.0 which usually comes in the very end of settings.xml of IBI in the section, are again mx of potential and end of it, which should be larger than all our end table in each section. On Thursday, April 12, 2018 at 4:09:27 PM UTC-4, Christoph

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Christoph Junghans
On Thu, Apr 12, 2018 at 2:03 PM, Alexander Alexander wrote: > > Hi Christoph, > > I guess I found out what do you mean, I hope the attached bonded tables for > 3-bead system would be fine. Yeah these one look better, if you zoom around the minimum you should see some

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Christoph Junghans
On Thu, Apr 12, 2018 at 11:26 AM, Alexander Alexander wrote: > > Thanks. > > On Thursday, April 12, 2018 at 12:43:54 PM UTC-4, Christoph Junghans wrote: >> >> On Thu, Apr 12, 2018 at 9:57 AM, Alexander Alexander >> wrote: >> > >> > >> > On

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Alexander Alexander
Hi Christoph, I guess I found out what do you mean, I hope the attached bonded tables for 3-bead system would be fine. Best regards, Alex On Thursday, April 12, 2018 at 1:26:37 PM UTC-4, Alexander Alexander wrote: > > > Thanks. > > On Thursday, April 12, 2018 at 12:43:54 PM UTC-4, Christoph

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Alexander Alexander
Thanks. On Thursday, April 12, 2018 at 12:43:54 PM UTC-4, Christoph Junghans wrote: > > On Thu, Apr 12, 2018 at 9:57 AM, Alexander Alexander > wrote: > > > > > > On Thursday, April 12, 2018 at 8:14:42 AM UTC-4, Christoph Junghans > wrote: > >> > >> On Thu, Apr 12,

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Christoph Junghans
On Thu, Apr 12, 2018 at 9:57 AM, Alexander Alexander wrote: > > > On Thursday, April 12, 2018 at 8:14:42 AM UTC-4, Christoph Junghans wrote: >> >> On Thu, Apr 12, 2018 at 3:39 AM, Alexander Alexander >> wrote: >> > >> > Hi, >> > >> > I was

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Alexander Alexander
On Thursday, April 12, 2018 at 8:14:42 AM UTC-4, Christoph Junghans wrote: > > On Thu, Apr 12, 2018 at 3:39 AM, Alexander Alexander > wrote: > > > > Hi, > > > > I was wondering if it is normal to have table_b1,2,3,4.xvg like the > attached > > figures? They are the

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Christoph Junghans
On Thu, Apr 12, 2018 at 3:39 AM, Alexander Alexander wrote: > > Hi, > > I was wondering if it is normal to have table_b1,2,3,4.xvg like the attached > figures? They are the result if BI (similar script as hexane example) over a > 500 ns nvt simulation of a single

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-12 Thread Alexander Alexander
Hi, I was wondering if it is normal to have table_b1,2,3,4.xvg like the attached figures? They are the result if BI (similar script as hexane example) over a 500 ns nvt simulation of a single molecule. What could be the meaning of the straight line passing from point (0,0) in table_b1.xvg

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-11 Thread Christoph Junghans
On Wed, Apr 11, 2018 at 12:49 PM, Alexander Alexander wrote: > > Hi Christoph, > > On Wednesday, April 11, 2018 at 8:22:24 AM UTC-4, Christoph Junghans wrote: >> >> >> >> On Wed, Apr 11, 2018, 01:51 Alexander Alexander >> wrote: >>> >>> >>> Hi,

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-11 Thread Alexander Alexander
Hi Christoph, On Wednesday, April 11, 2018 at 8:22:24 AM UTC-4, Christoph Junghans wrote: > > > > On Wed, Apr 11, 2018, 01:51 Alexander Alexander > wrote: > >> >> Hi, >> You mean BI over a single molecule in vacuum? >> > > Yes, or any potential, which has right

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-11 Thread Christoph Junghans
On Wed, Apr 11, 2018, 01:51 Alexander Alexander wrote: > > Hi, > You mean BI over a single molecule in vacuum? > Yes, or any potential, which has right equilibrium length/value. > Instead of sd integrater can md integrator (but still in NVT ensemble) be > used in

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-11 Thread Alexander Alexander
Hi, You mean BI over a single molecule in vacuum? Instead of sd integrater can md integrator (but still in NVT ensemble) be used in IBI ( bonded and nonbonded or either of them) and still have good results? Thanks, Alex -- You received this message because you are subscribed to the Google

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-10 Thread Christoph Junghans
On Tue, Apr 10, 2018 at 2:50 PM, Alexander Alexander wrote: > > Hi Christoph, > > On Tuesday, April 10, 2018 at 4:28:30 PM UTC-4, Christoph Junghans wrote: >> >> On Sun, Apr 8, 2018 at 8:17 PM, Alexander Alexander >> wrote: >> > >> > Thanks

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-10 Thread Alexander Alexander
Hi Christoph, On Tuesday, April 10, 2018 at 4:28:30 PM UTC-4, Christoph Junghans wrote: > > On Sun, Apr 8, 2018 at 8:17 PM, Alexander Alexander > wrote: > > > > Thanks Christoph. > > > > I know they are zero, and > > > >> wrote: > >> > > >>

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-10 Thread Christoph Junghans
On Sun, Apr 8, 2018 at 8:17 PM, Alexander Alexander wrote: > > Thanks Christoph. > > I know they are zero, and > >> wrote: >> > >> > Dear all, >> > >> > The potential_shift.pl crashes in IBI for some of the bond and angles in >> > step 5, I have

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-09 Thread Christoph Scherer
Hi, I just read the message and looked into the files. In my opinion, the issue is the same than above. The file bond-RB-RA.dist.new contains only 0s and therefore dpot.pure_ibi has no valid entries. The setup looks okay to me. I also rerun the gromacs simulation with the tabulated potentials

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-08 Thread Alexander Alexander
On Sunday, April 8, 2018 at 10:17:56 PM UTC-4, Alexander Alexander wrote: > > > Thanks Christoph. > > I know they are zero, and > > wrote: >> > >> > Dear all, >> > >> > The potential_shift.pl crashes in IBI for some of the bond and angles >> in >> > step 5, I have

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-08 Thread Alexander Alexander
Thanks Christoph. I know they are zero, and wrote: > > > > Dear all, > > > > The potential_shift.pl crashes in IBI for some of the bond and angles > in > > step 5, I have already seen a suggestion in mailing list such that "one > > should pick the minimum of the

Re: [votca] potential_shift.pl --type angle failed in step 5

2018-04-08 Thread Christoph Junghans
On Sun, Apr 8, 2018 at 5:35 PM, Alexander Alexander wrote: > > Dear all, > > The potential_shift.pl crashes in IBI for some of the bond and angles in > step 5, I have already seen a suggestion in mailing list such that "one > should pick the minimum of the interaction