Re: [gmx-users] Validation of molecular dynamic simulation results

2014-02-11 Thread Marcelo Depólo
regards, -- Marcelo Depólo Polêto Uppsala Universitet - Sweden -- 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

Re: [gmx-users] Long trajectory split

2014-02-23 Thread Marcelo Depólo
But it is not quite happening simultaneously, Justin. It is producing one after another and, consequently, backing up the files. -- 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

Re: [gmx-users] Long trajectory split

2014-02-23 Thread Marcelo Depólo
: are you sure that your binary is parallel? how many frames do those trajectory files contain? Dr. Vitaly V. Chaban On Sun, Feb 23, 2014 at 5:32 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Maybe I should explain it better. I am using *mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o

Re: [gmx-users] Long trajectory split

2014-02-23 Thread Marcelo Depólo
the .mdp files were copied from a sucessful folder. But thank you both for the support. 2014-02-23 20:20 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Sun, Feb 23, 2014 at 6:48 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Justin, the other runs with the very same binary do

Re: [gmx-users] Long trajectory split

2014-02-27 Thread Marcelo Depólo
have incorrect parallelism in this case. Can you post all the files you obtain for people to inspect? Dr. Vitaly V. Chaban On Sun, Feb 23, 2014 at 9:04 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Justin, as far as I realized, the next log file starts at 0ps what would mean

Re: [gmx-users] RDF analysis with respect to center of mass of otein

2014-09-19 Thread Marcelo Depólo
/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. -- Marcelo Depólo Polêto Biochemicist

[gmx-users] Atom-barycenter distance

2014-11-24 Thread Marcelo Depólo
Hi guys! Consider the atoms 1, 2 and 3 forming a triangle: I was wondering how can I calculate the barycenter of this triangle using the atoms coordinates? I want to measure the distance through time but I am not sure if there is a simple way to do it. Cheers! -- Marcelo Biochemicist

Re: [gmx-users] RDF calculation.

2014-12-27 Thread Marcelo Depólo
...@gromacs.org. -- Marcelo Depólo Polêto Biochemicist University of Viçosa - Brazil -- 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

Re: [gmx-users] DNA-protein complex

2015-03-18 Thread Marcelo Depólo
the protocol that you have used. Just the production mdp file will not provide enough info to say anything. Please send your protocol and mdp files. Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil

Re: [gmx-users] DNA-protein complex

2015-03-17 Thread Marcelo Depólo
files, so as your force field that you have choose. It is hard to say anything without more details. Also, what do you mean by 'unwinding'? Could you be more specific? Thank you in advance for your suggestions. best regards Urszula Cheers! -- Marcelo Depólo Polêto B.Sc. Biochemistry

Re: [gmx-users] Carbohydrate force fields in GROMACS

2015-03-20 Thread Marcelo Depólo
2015-03-20 14:21 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 3/20/15 1:16 PM, Marcelo Depólo wrote: As my previous email said: there is a modified GROMOS forcefield for carbohydrated. Install it and check out which kind of modifications on topologies you should do. Install it, sure

Re: [gmx-users] Carbohydrate force fields in GROMACS

2015-03-20 Thread Marcelo Depólo
There is also a Modified GROMOS forcefield for glycans here: http://dx.doi.org/10.1021/ct300479h Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search

Re: [gmx-users] Carbohydrate force fields in GROMACS

2015-03-20 Thread Marcelo Depólo
or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] genbox + python bug?

2015-03-13 Thread Marcelo Depólo
Thanks for the insights, Mark. It was a 'aprun' issue. When I remove it from the command, everything worked out. -- Marcelo 2015-03-13 14:10 GMT-03:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hey, I have

[gmx-users] genbox + python bug?

2015-03-13 Thread Marcelo Depólo
python and genbox? Does anyone has a suggestion? -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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

[gmx-users] Fluorine Gromos LJ parameters

2015-04-01 Thread Marcelo Depólo
Hi, I've done an extensively search out the web but I could not find LJ parameters for Fluoride (ionic). Gromos54A7 has only Fluorine parameters. Does anyone knows any new parameters for that? Best regards! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil

[gmx-users] Maximum Force constant for Position Restraints

2015-04-21 Thread Marcelo Depólo
Hi guys! Is there a maximum value of Force Constant for Position restraints? Reading the Manual I could only find the default and the equation to describe it. Best, -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology

Re: [gmx-users] Maximum Force constant for Position Restraints

2015-04-21 Thread Marcelo Depólo
. The coefficient is four because of the Nyquist theorem. I believe GMX tests for high vibrational frequencies according to 20*pi*tau on the left (ten times the period). Hope this helps. Alex On Tue, Apr 21, 2015 at 1:02 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hi

[gmx-users] Position restraint for ions

2015-04-14 Thread Marcelo Depólo
this as an error. Would someone knows a neat way to do this? Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] A query

2015-04-13 Thread Marcelo Depólo
Nope! They are just for our amusement. Maybe only one has to do it: Check your input! David van der Spoel Cheers! Marcelo Depólo Em 13/04/2015 07:05, Priya Das priyadas...@gmail.com escreveu: Dear All, *gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili Peppers

Re: [gmx-users] Position restraint for ions

2015-04-14 Thread Marcelo Depólo
, MD 21201 -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Position restraint for ions

2015-04-14 Thread Marcelo Depólo
2015-04-14 14:54 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 4/14/15 1:48 PM, Marcelo Depólo wrote: Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group non-Water

Re: [gmx-users] Position restraint for ions

2015-04-14 Thread Marcelo Depólo
2015-04-14 17:26 GMT-03:00 Justin Lemkul jalem...@vt.edu On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section

Re: [gmx-users] simulating liquid SO2 (Sulphur dioxide)

2015-04-05 Thread Marcelo Depólo
Em 05/04/2015 14:44, Jashimuddin Ashraf jashimuddin.ashra...@gmail.com escreveu: Dear gromacs users, I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create an equilibrated structure of SO2 molecules using the gmx insert-molecules function. As I try to minimize the energy

[gmx-users] Explicit Hydrogen LJ param

2015-06-15 Thread Marcelo Depólo
-05 1.5129e-08 H1 0.000 0.000 A 0 0 Best regards, -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil

[gmx-users] Fatal error: Index contains atom numbers larger than the topology

2015-08-20 Thread Marcelo Depólo
14000 elementsGroup 2 (ANI) has 14000 elementsSelect a group: 0---Program g_dos_506, VERSION 5.0.6Fatal error:Index contains atom numbers larger than the topology* Does anyone have an idea about it? Cheers! -- Marcelo Depólo Polêto

Re: [gmx-users] gromacs 5 pdb2gmx does not faithfully reproduce the AMBER99sb-ILDN force field

2015-07-22 Thread Marcelo Depólo
Em 22/07/2015 14:51, Christopher Neale chris.ne...@alum.utoronto.ca escreveu: Dear Users: I believe that gromacs 5 pdb2gmx does not faithfully reproduce the AMBER99sb-ILDN force field. It is not exclusive behavior for any particular FF. I've got same error for Gromos54a7. If one uses multiple

[gmx-users] gmx dos - Possible bug on 5.0.6

2015-08-25 Thread Marcelo Depólo
! -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Calculation of Cv

2015-08-31 Thread Marcelo Depólo
acs 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)subscri

Re: [gmx-users] gmx dos - Possible bug on 5.0.6

2015-08-25 Thread Marcelo Depólo
2015-08-25 17:29 GMT-03:00 David van der Spoel sp...@xray.bmc.uu.se: On 25/08/15 18:24, Marcelo Depólo wrote: Hi all! I've been running gmx dos (version 5.0.4) in some trajectories with the following: echo BEN | gmx_504 dos -s ben.DOS.tpr -f ben.DOS.trr -g ben.log -dos dos.xvg -vacf

Re: [gmx-users] K+ ions instead of NA+ for neutralization

2015-09-13 Thread Marcelo Depólo
polyelectronic biomolecules (nucleic acids and membranes), widely reported. I would check this cases before designing any simulation Cheers, -- Marcelo Depólo Polêto Structural Bioinformatics Group Master Student - BCM/UFRGS B.Sc. Biochemistry - UFV Em 13/09/2015 09:42, "Vitaly V. Chaban" <vvcha

Re: [gmx-users] Density of States syntax question

2016-05-31 Thread Marcelo Depólo
re > 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. > -- -- Marcelo Depólo Polêto M

[gmx-users] Hbond residence time

2017-04-24 Thread Marcelo Depólo
of what each of these types mean? Thanks in advance! -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone: + 55 51 3308-7770 -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Donors and Acceptors - gmx hbond

2017-08-10 Thread Marcelo Depólo
he h-bonds donated by H atom and accepted by the O atom at the same time? If so, is there anyway to calculate both separately? Cheers! -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone: + 55 51

Re: [gmx-users] Donors and Acceptors - gmx hbond - gromacs.org_gmx-users Digest, Vol 160, Issue 67

2017-08-14 Thread Marcelo Depólo
; I would use the selection groups judiciously, for example have one of them > with only donor atoms in it. > > Mark > > -- -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone

Re: [gmx-users] HBond for F and S (Justin Lemkul)

2017-04-24 Thread Marcelo Depólo
Thanks, Justin! It worked just fine. I guess using a flag to include different atomtypes into the analyses would be a nice feature for next GROMACS versions. Cheers! -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center

[gmx-users] HBond for F and S

2017-04-24 Thread Marcelo Depólo
Hi, Can gmx hbond also calculates hbonds between non-canonical atoms like S or F as well? If so, how can I do it? Cheers! -- Marcelo -- 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

[gmx-users] atomname2types.n2t explanation

2017-05-23 Thread Marcelo Depólo
Hi Can someone explain what does each column on atomname2types.n2t mean? For gromos53a5 it is: H H0.408 1.008 1 O 0.1 O OA -0.674 15.9994 2 C 0.14 H 0.1 C CH3 0.000 15.0351 C 0.15 C CH0 0.266 12.0114 C 0.15 C 0.15 C 0.15

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

2017-05-25 Thread Marcelo Depólo
Hi, I had the same struggle benchmarking a similar system last week. Just for curiosity, could you tell us the performance you get when sharing your GPU with multiple jobs? In my case (6k atoms + Reaction field + 8 cores 2.2Ghz + TitanX Pascal), I've got ~440 ns/day. However, I get ~280 ns/day

[gmx-users] gmx hbond -tu error

2017-05-01 Thread Marcelo Depólo
Hi! I am running ACF calculations in gmx hbond tool in 5.0.7 version. When running: gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg and gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg The results given for the ACF are completely different (example:

[gmx-users] gmx sorient interpretation

2017-05-01 Thread Marcelo Depólo
Hi, I am not sure how to interpret the cos(theta1) around my reference atom. The help printed is not straightforward when comes to set which atoms forms the angle theta1. For instance. "theta_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms

[gmx-users] cmaptypes format

2020-01-15 Thread Marcelo Depólo
Hi everyone! I was wondering about the cmaptypes format within cmap.itp file. [ cmaptypes ] C N CT C N 1 24 24\ I understand that C-N-CT-C = phi, N-CT-C-N = psi and 24x24 is the grid size. What does this '1' mean? Thanks in advance! -- Marcelo Depólo Polêto Postdoctoral Researcher BIOAGRO

[gmx-users] Residue-Specific CMAPS in GROMACS

2020-01-17 Thread Marcelo Depólo
Hi all, I've been investigating the implementation of CMAP in GROMACS and, as far as I understood, the current CMAP format does not allow the use of residue-specific CMAPS, since it is based on atomtypes and not on function numbers, as GROMACS normally do. For example, for AMBER, the function

Re: [gmx-users] CMAP format on GROMACS

2020-01-08 Thread Marcelo Depólo
3129 > http://www.thelemkullab.com > > ========== > > > > -- > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] CMAP format on GROMCACS

2020-01-06 Thread Marcelo Depólo
r that its "y-axis" would be PSI and "x-axis" would be PHI? Cheers! -- Marcelo Depólo Polêto Postdoctoral Researcher BIOAGRO - Room T07 Department of General Biology - UFV Contact: + 55 31 3612-2464 -- Gromacs Users mailing list * Please search the archive at http://www.gro