[gmx-users] RE: 2D umbrella sampling simulation

Dear Chris, Thanks for your check. Yes, it should be pull_group2 for C. In this case, the two distances have a reference group B. What about the case in which no common reference group is shared with the two distances, e.g. distance1 is defined as A-B and distance2 as C-D? Can current gromac

[gmx-users] 2D umbrella sampling simulation

Your restraint involving group C should use pull_group2, etc, not another copy of pull_group1. Other than that, it looks like a valid approach. Chris. -- original message -- I am going to perform the two-dimensional umbrella sampling using a pair of distances (the distance btw atoms A and

Re: [gmx-users] Re: a new GROMACS simulation tool

Hi Kevin, Thanks. Houyang On Thu, Oct 24, 2013 at 3:00 PM, sri2201 wrote: > Hi > I would like to try it out > > Srinivasa Rao Penumutchu > Research Scholar > Protein NMR Lab , II floor-218 > Department of Chemistry > National Tsing Hua University, > Hsinchu, Taiwan. > Ph: 886357151-35605, > Emai

[gmx-users] Re: a new GROMACS simulation tool

Hi I would like to try it out Srinivasa Rao Penumutchu Research Scholar Protein NMR Lab , II floor-218 Department of Chemistry National Tsing Hua University, Hsinchu, Taiwan. Ph: 886357151-35605, Email- penumutchu.srini...@gmail.com ,s9923...@m99.nthu.edu.tw -- View this message in contex

Re: [gmx-users] TFE-water simulation

On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but

Re: [gmx-users] nstcalclr bug?

Thanks! I get confused because mdout.mdp was different from the output of gmxdump. And Messaggio inviato dal mio ASUS MeMO Pad Mark Abraham ha scritto: Ja. No twin-range => no long-range :-) Mark On Thu, Oct 24, 2013 at 5:50 PM, wrote: > I think nstcalclr would only do something if you

Re: [gmx-users] TFE-water simulation

Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me so

[gmx-users] 2D umbrella sampling simulation

Dear GMX users, I am going to perform the two-dimensional umbrella sampling using a pair of distances (the distance btw atoms A and B, C and B) in the restraints. Could someone please tell whether I can use the current pull code as follows? - ; Pu

[gmx-users] gmxdump segmentation fault

I have a user that is using gromacs 4.5.6 and they get a segmentation fault when using gmxdump. I just built the latest version of gromacs 4.6.3 for them in case something had been fixed, but still get the segmentation fault. Following is the output from the command. Is there a limit to the s

Re: [gmx-users] Re: meaning of the parameters in gbsa.itp

On Thu, Oct 24, 2013 at 6:24 PM, Corina Mo wrote: > Dear Justin, > > Thanks again! Will look into it. > Btw, you know if there is any plan to implement implicit lipid model in > GROMACS? > No plans known. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

Re: [gmx-users] pbc problem

As Justin said, there is no actual division between region 1 and 4. Apparently you got the free diffusion you asked for! :-) Mark On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati wrote: > Dear Mark > > Thank for your reply. > > If I show my system as 4 regions, my system before equilibration is

[gmx-users] Re: meaning of the parameters in gbsa.itp

Dear Justin, Thanks again! Will look into it. Btw, you know if there is any plan to implement implicit lipid model in GROMACS? Corina On Fri, Oct 25, 2013 at 12:17 AM, Justin Lemkul [via GROMACS] < ml-node+s5086n5011968...@n6.nabble.com> wrote: > > > On 10/24/13 12:11 PM, Coco Mo wrote: > > Th

Re: [gmx-users] nstcalclr bug?

Ja. No twin-range => no long-range :-) Mark On Thu, Oct 24, 2013 at 5:50 PM, wrote: > I think nstcalclr would only do something if you have longer range > interactions to calculate (lr means longer than rlist). Therefore > something has be longer than rlist for this to happen. > > > Hi there,

Re: [gmx-users] Output pinning for mdrun

On Thu, Oct 24, 2013 at 4:52 PM, Carsten Kutzner wrote: > On Oct 24, 2013, at 4:25 PM, Mark Abraham > wrote: > > > Hi, > > > > No. mdrun reports the stride with which it moves over the logical cores > > reported by the OS, setting the affinity of GROMACS threads to logical > > cores, and warning

Re: [gmx-users] meaning of the parameters in gbsa.itp

On 10/24/13 12:11 PM, Coco Mo wrote: Thanks Justin for the quick hint! So, only the last two columns are needed. Sorry for the stupid question, where can I obtain reliable values for the atomic van der waals radii? Is it I have to calculate from the original force field parameters, in my case,

Re: [gmx-users] Output pinning for mdrun

Hi Carsten, On Thu, Oct 24, 2013 at 4:52 PM, Carsten Kutzner wrote: > On Oct 24, 2013, at 4:25 PM, Mark Abraham wrote: > >> Hi, >> >> No. mdrun reports the stride with which it moves over the logical cores >> reported by the OS, setting the affinity of GROMACS threads to logical >> cores, and wa

Re: [gmx-users] meaning of the parameters in gbsa.itp

On 10/24/13 12:02 PM, Corina Mo wrote: Dear Gromacs users, I am interested to do implicit solvent MD but I find that some atoms (atomtype opls_961-965) in my system does not have parameters in the file gbsa.itp. Does anyone know the meaning of these columns in the file and the proper way to d

[gmx-users] meaning of the parameters in gbsa.itp

Dear Gromacs users, I am interested to do implicit solvent MD but I find that some atoms (atomtype opls_961-965) in my system does not have parameters in the file gbsa.itp. Does anyone know the meaning of these columns in the file and the proper way to derive these values? ; atypesarst

Re: [gmx-users] meaning of the parameters in gbsa.itp

Thanks Justin for the quick hint! So, only the last two columns are needed. Sorry for the stupid question, where can I obtain reliable values for the atomic van der waals radii? Is it I have to calculate from the original force field parameters, in my case, the opls? Corina On Fri, Oct 25, 2013

Re: [gmx-users] nstcalclr bug?

I think nstcalclr would only do something if you have longer range interactions to calculate (lr means longer than rlist). Therefore something has be longer than rlist for this to happen. > Hi there, > > I am using gromacs-4.6.1 with this mdp file: > > integrator= md; leap-frog int

[gmx-users] nstcalclr bug?

Hi there, I am using gromacs-4.6.1 with this mdp file: integrator = md; leap-frog integrator nsteps = 300 ; 6.0 ns dt = 0.002 ; 2 fs nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save veloc

Re: [gmx-users] pbc problem

On 10/24/13 10:57 AM, shahab shariati wrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibratio

[gmx-users] pbc problem

Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters regi

Re: [gmx-users] Output pinning for mdrun

On Oct 24, 2013, at 4:25 PM, Mark Abraham wrote: > Hi, > > No. mdrun reports the stride with which it moves over the logical cores > reported by the OS, setting the affinity of GROMACS threads to logical > cores, and warnings are written for various wrong-looking cases, but we > haven't taken th

Re: [gmx-users] Output pinning for mdrun

Hi, No. mdrun reports the stride with which it moves over the logical cores reported by the OS, setting the affinity of GROMACS threads to logical cores, and warnings are written for various wrong-looking cases, but we haven't taken the time to write a sane report of how GROMACS logical threads an

Re: [gmx-users] Genion error

On 10/24/13 10:21 AM, felipe vasquez wrote: Hi, I chose group 0 (System), but I also tried others like 1 (Protein) or 2 (Protein+H) with the same result. You don't want to embed ions into your protein or haphazardly into the system. You'll start deleting random segments of molecules, or th

Re: [gmx-users] Genion error

Hi, I chose group 0 (System), but I also tried others like 1 (Protein) or 2 (Protein+H) with the same result. Regards, Andrés F. *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública In

Re: [gmx-users] Genion error

On 10/24/13 9:34 AM, felipe vasquez wrote: Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. What group did you choose at the genion prompt? The command I entered in this step

[gmx-users] Genion error

Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. The command I entered in this step was: genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+ -nname CL- How c

Re: [gmx-users] Gromos54a8

Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul wrote: > > > On 10/24/13 9:00 AM, rajat desikan wrote: > >> Hi Justin, >> Thanks for the comments. >> >> Since the script was written in 2009, I don't want to

Re: [gmx-users] Gromos54a8

On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. "The same would apply here - if you want to validate b

Re: [gmx-users] Gromos54a8

Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. "The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs." I didn't re

Re: [gmx-users] Gromos54a8

On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from Convert

Re: [gmx-users] cant find certain atomtypes from atomtype database

On 10/24/13 1:03 AM, JuYeon wrote: dear gromacs users im using gromacs to make CS2 MD programs i made pdb file (by converting mol file to pdb file) and rtp file for CS2this is what i made COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.2HETATM1 C LIG 1 19.882 -4.263

Re: [gmx-users] g_hbond and g_rdf in vacuum

"Not working" is too vague a symptom for anyone to guess what the problem is, sorry. Mark On Oct 24, 2013 9:39 AM, "Santu Biswas" wrote: > dear users, > > I am performing 500ps mdrun in vacuum for polypeptide(formed > by 10-residues leucine) using gromacs_4.5.5(double-precision) us

Re: [gmx-users] pbc problem

On Oct 24, 2013 8:10 AM, "shahab shariati" wrote: > > Dear jkrieger > > I used 2 times trjconv tool: > > 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump > > 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center > > > Dear Mark > > I selected all lipid at

[gmx-users] Gromos54a8

Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgz

[gmx-users] Output pinning for mdrun

Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don'

[gmx-users] g_hbond and g_rdf in vacuum

dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double-precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cp