Re: [votca] Tabulated vs harmonic potential for a bond

Hi Christoph, Any idea, please? On Thursday, May 3, 2018 at 5:50:15 PM UTC-4, Alexander Alexander wrote: > > > > On Thursday, May 3, 2018 at 4:56:25 PM UTC-4, Christoph Junghans wrote: >> >> On Thu, May 3, 2018 at 1:46 PM, Alex <alexand...@gmail.com> wrote: >&

[votca] Convergence

Hi all, My considered convergence criteria defined in my settings.xml for a IBI-Nonbonded is as follow: default 0.5 and now the number in *.dist.conv for all of the nonbonded interactions, just are oscillating around 1.0 and no sensible improvement any more I

[votca] Martini water

Dear all, I was wondering what the correct usage of martinize.py is for mapping a atomistic water.gro file to the P4 water martini coarse grained? The "martinize.py -f AA-water.gro -x CG-water.gro ... " gives me only a box of the system. How about when I have system including two type of

[votca] Tabulated vs harmonic potential for a bond

Dear all, I did a My IBI-bonded-nonbonded (after getting the nonbonded potentials via IBI-nonbonded only) crashes dues to the "...bonded interactions could not be calculated because some atoms involved moved further apart ...". By replacing the ill-bond by a harmonic potential in topol.top

Re: [votca] Tabulated vs harmonic potential for a bond

Hi Christoph, Thanks. On Wednesday, May 2, 2018 at 5:13:13 PM UTC-4, Christoph Junghans wrote: > > On Wed, May 2, 2018 at 1:38 PM, Alexander Alexander > <alexand...@gmail.com > wrote: > > Dear all, > > I did a > > My IBI-bonded-nonbonded (after getting the

Re: [votca] Tabulated vs harmonic potential for a bond

Thanks. On Wednesday, May 2, 2018 at 5:54:50 PM UTC-4, Christoph Junghans wrote: > > On Wed, May 2, 2018 at 3:37 PM, Alexander Alexander > <alexand...@gmail.com > wrote: > > Hi Christoph, > > Thanks. > > > > On Wednesday, May 2, 2018 at 5:1

Re: [votca] Error: ... Some atoms involved moved further apart

Thank Christoph. On Thursday, April 26, 2018 at 10:49:25 AM UTC-4, Christoph Junghans wrote: > > On Thu, Apr 26, 2018 at 1:37 AM, Alexander Alexander > <alexand...@gmail.com > wrote: > > > > Dear all, > > Using IBI over nonbonded parameters I intend to p

Re: [votca] Error: ... Some atoms involved moved further apart

Hi, On Thursday, April 26, 2018 at 12:23:36 PM UTC-4, Christoph Junghans wrote: > > On Thu, Apr 26, 2018 at 9:12 AM, Alexander Alexander > <alexand...@gmail.com > wrote: > > Thank Christoph. > > > > On Thursday, April 26, 2018 at 10:49:25 AM U

[votca] Error: ... Some atoms involved moved further apart

Dear all, Using IBI over nonbonded parameters I intend to parameterize the CG parameter for a molecule which has 3 beads in 2 types. The initial CG-configuration.gro was extracted from the trajectory of an atomistic simulation over the system which I am pretty sure that it has been enough

Re: [votca] Tabulated vs harmonic potential for a bond

Hi Christoph, On Wednesday, May 2, 2018 at 9:29:51 PM UTC-4, Christoph Junghans wrote: > > On Wed, May 2, 2018 at 4:37 PM, Alexander Alexander > <alexand...@gmail.com > wrote: > > Thanks. > > > > On Wednesday, May 2, 2018 at 5:54:50 PM UTC-4, Christoph Jungha

Re: [votca] Tabulated vs harmonic potential for a bond

> >> > >> On Thu, May 3, 2018 at 12:44 PM, Alexander Alexander > >> <alexand...@gmail.com > wrote: > >> > Hi Christoph, > >> > > >> > On Wednesday, May 2, 2018 at 9:29:51 PM UTC-4, Christoph Junghans > wrote: > >&g

Re: [votca] a table.xvg is missing

, Christoph Junghans wrote: > > On Tue, Apr 3, 2018 at 11:05 PM, Alexander Alexander > <alexand...@gmail.com > wrote: > > Thank you Christoph. > > > > The gmx_mpi mdrun crashed in the step_001, with the below error; > > > > Tabulated interaction of type 'T

Re: [votca] a table.xvg is missing

Dear Christoph, On Thursday, April 5, 2018 at 6:46:13 AM UTC-4, Christoph Junghans wrote: > > On Wed, Apr 4, 2018 at 5:52 PM, Alexander Alexander > <alexand...@gmail.com > wrote: > > Thanks Christoph. > > > > Finally my IBI (both bond

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

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 > <alexand...@gmail.com > wrote: > > > > Thanks Christoph. > > > > I know they are zero, and

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

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

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 <alexand...@gmail.com > > wrote: > >> >> Hi, >> You mean BI over a single molecule in vacuum? >

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

for example? Also, is the format of the table_bonded.xvg is "x y [error bar]"? Thank you. Regards, Alex On Wednesday, April 11, 2018 at 3:44:30 PM UTC-4, Christoph Junghans wrote: > > On Wed, Apr 11, 2018 at 12:49 PM, Alexander Alexander > <alexand...@gmail.com > wrot

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

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 > <alexand...@gmail.com > wrote: > > > > Hi, > > > > I was wondering if it is normal to have table_b1,2,3,

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

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 > <alexand...@gmail.com > wrote: > > > > > > On Thursday, April 12, 2018 at 8:14:42 AM UTC-4, Christoph Junghans &g

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

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 U

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

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 > <alexand...@gmail.com > wrote: > > > > Thank you. > > > > An then these parameter > > 1000 >

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

On Sunday, April 8, 2018 at 10:17:56 PM UTC-4, Alexander Alexander wrote: > > > Thanks Christoph. > > I know they are zero, and > > <alexand...@gmail.com> wrote: >> > >> > Dear all, >> > >> > The potential_shift.pl crashes in

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

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

[votca] Exclusion list

Dear all, In CG parametrisation of one of my molecule which has 45 atoms, using *BI for bonded and IBI for nonbonded parameters*, a 900 ns simulation of the single molecule in vacuum has been already completed while I forgot including the exclusions list gotten from csg_boltzmann in to my

Re: [votca] Exclusion list

Hi Any ideas please? Regards, Alex -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to

Re: [votca] Exclusion list

Hi Christoph, On Thursday, April 19, 2018 at 12:19:49 AM UTC-4, Christoph Junghans wrote: > > On Wed, Apr 18, 2018 at 9:39 PM, Alexander Alexander > <alexand...@gmail.com > wrote: > > Hi > > Any ideas please? > Sorry, there was no question in your previous emai

[votca] ibi-all after ibi-nonbonded

Dear all, After successfully doing IBI over nonbonded parameter of my system cantoning 3 beads-3 type, I am doing IBI on both bonded and nonbonded together. The system has 2 bonds and one angle. As the attached figure shows all of the bonded parameters (two bonds and one angle) getting worse

Re: [votca] Re: Mismatched tag

to obtain all of the CG parameters of the molecule of my interest. Thank you very much. Best regards, Alex On Tuesday, March 27, 2018 at 4:55:51 PM UTC-4, Christoph Junghans wrote: > > On Tue, Mar 27, 2018 at 2:07 PM, Alexander Alexander > <alexand...@gmail.com > wrote: >

[votca] Mismatched tag

Dear all, The "csg_dump --top case.tpr --cg case.xml" parses error at the last line of my case.xml with the mismatched tag, I can not find out where I am doing wrong, so, I would be so appreciated if you could have a look at my attached case.xml,.top,gro files and help me overcome the issue.

Re: [votca] Re: Mismatched tag

t 4:51:53 AM UTC-4, Christoph Junghans wrote: > > On Thu, Mar 29, 2018 at 12:14 PM, Alexander Alexander > <alexand...@gmail.com > wrote: > > Thank you. > > > > On Thursday, March 29, 2018 at 1:31:52 PM UTC-4, Christoph Junghans > wrote: > >> > >&

Re: [votca] Re: Mismatched tag

ards, Alex On Wednesday, March 28, 2018 at 3:28:44 AM UTC-4, Christoph Junghans wrote: > > On Tue, Mar 27, 2018 at 6:28 PM, Alexander Alexander > <alexand...@gmail.com > wrote: > > > > Thank Christoph. > > Actually the xmlwf did not give more information th

Re: [votca] Re: Mismatched tag

Thank you. On Thursday, March 29, 2018 at 1:31:52 PM UTC-4, Christoph Junghans wrote: > > On Thu, Mar 29, 2018 at 10:25 AM, Alexander Alexander > <alexand...@gmail.com > wrote: > > > > Thanks. > > I would be so thankful if one could comment on below question

Re: [votca] a table.xvg is missing

r map.xml? in other words, should we define both A B and B A ? Thanks for your time in advance. Best regards, Alex On Tuesday, April 3, 2018 at 5:29:00 AM UTC-4, Christoph Junghans wrote: > > > > On Tue, Apr 3, 2018, 09:31 Alexander Alexander <alexand...@gmail.com > > w

Re: [votca] Re: Mismatched tag

Hi Christoph, Thank you again. On Saturday, March 31, 2018 at 5:02:49 AM UTC-4, Christoph Junghans wrote: > > On Fri, Mar 30, 2018 at 9:34 AM, Alexander Alexander > <alexand...@gmail.com > wrote: > > > > Dear Christoph, > > > > Thank you for your info

[votca] Re: Mismatched tag

Solved now, I was missing a backslash in . Anyway, thank you. Regards, Alex On Tuesday, March 27, 2018 at 2:20:10 PM UTC-4, Alexander Alexander wrote: > > > Dear all, > > The "csg_dump --top case.tpr --cg case.xml" parses error at the last line > of my case.xml wi