Re: [gmx-users] regarding nacl simulation in water using tabulated potentials

On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote: i had followed the instructions in themnaual for ninbonded interactions adn had created two tables one for nacl adn other table for water ion interations... That's not "I really don't have any idea on how to do this". Please ask the question yo

[gmx-users] freeze the carbonyl carbon atoms

Hi: I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is attached to one carbon atom of the CNT to form a carbonyl group. All the carbon atoms are supposed to be fixed, while carbonyl carbon a

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi Justin, I used 15 nm cubic box and 6 nm shell. I again tried to insert only 1 histidine molecule in the sphere. I get the same error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smalle

[gmx-users] problem while running grompp command

Hi all. I am doing dynamics studies of protein-ligand dynamics.When I am running grompp command error is coming "atomtype SDMSO NOT FOUND" . I checked in drg.itp file [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OM 1 LIG OXT 1 -0.758 15.9994 2 C 1 LIG C 1 0.362 12.0110 3 OM 1 LIG O 1 -0.

Re: [gmx-users] problem while running grompp command

rashi parihar wrote: Hi all. I am doing dynamics studies of protein-ligand dynamics.When I am running grompp command error is coming "atomtype SDMSO NOT FOUND" . I checked in drg.itp file [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OM 1 LIG OXT 1 -0.758 15.9994 2 C 1 LIG C 1 0.36

Re: [gmx-users] freeze the carbonyl carbon atoms

toby1024 wrote: Hi: I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is attached to one carbon atom of the CNT to form a carbonyl group. All the carbon atoms are supposed to be fixed

[gmx-users] Re: gmx-users Digest, Vol 85, Issue 65

n list for GROMACS users > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > dear gmx users, > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110509/2

Re: [gmx-users] liquid/liquid

Maria Hamilton wrote: Hi Prof. Mark Abraham I recived a tutorial from you that in the tutorial 3th molecule was one and there is not some of the 3th molecules that distributed randomly. I will be very thankful if you introduce to me a tutorial about my work. Tutorials are not written to t

Re: [gmx-users] ambar to opls force field

Hello Justin, In the J. Chem. Phys. paper author have run the simulation 6.5 ns. So I run the simulation 6.5 ns for collecting data and I have total 256 water molecules. NIlesh On Sun, May 8, 2011 11:58 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello Justin, >> >> >> Here I ha

Re: [gmx-users] ambar to opls force field

Nilesh Dhumal wrote: Hello Justin, In the J. Chem. Phys. paper author have run the simulation 6.5 ns. So I run the simulation 6.5 ns for collecting data and I have total 256 water molecules. I also asked how you calculated the dielectric constant. When trying to replicate others' work, it

[gmx-users] git server maintenance downtime

Hi, The git server may be temporarily offline today for maintenance. Cheers, Rossen -- 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'

Re: [gmx-users] freeze the carbonyl carbon atoms

On 9/05/2011 5:23 PM, toby1024 wrote: Hi: I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is attached to one carbon atom of the CNT to form a carbonyl group. All the carbon atoms are su

[gmx-users] Re: gmx-users Digest, Vol 85, Issue 67

I mean all the positions of the carbon atoms are invariant during mdrun. In the .gro file, carbonyl carbon and oxygen atoms are defined as group 'Carbonyl' and the rest every single carbon atom is defined as 'CNT'. For the use of 'freeze groups', the group 'CNT' should be freezed. But for group

Re: [gmx-users] ambar to opls force field

I used g_dipoles to calculate dielectric constant. g_dipoles -f water.trr -s water.tpr -eps Group 0 ( System) has 768 elements Group 1 ( Protein) has 768 elements Group 2 ( Protein-H) has 256 elements Group 3 ( C-alpha) has 0 elements Group 4 (Bac

[gmx-users] Re: freeze the carbonyl carbon atoms

ow > to deal with the carbonly atoms? Well if you're prepared to model the CNT frozen, why not freeze the oxygen bound to it? Anything else sounds like a recipe for more trouble. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs

Re: [gmx-users] frozen CNT with carbonyls

On 9/05/2011 10:43 PM, toby1024 wrote: Please use a useful subject line when replying to a digest. > I mean all the positions of the carbon atoms are invariant during > mdrun. In the .gro file, carbonyl carbon and oxygen atoms are defined > as group 'Carbonyl' and the rest every single carbon

Re: [gmx-users] Re: freeze the carbonyl carbon atoms

rouble. > Mark > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110509/1fa0aa57/attachment-0001.html > -- -- gmx-users mailing listgmx-users@gromacs.org htt

Re: [gmx-users] How to recenter solvent around solute

On Mon, May 9, 2011 at 1:39 AM, Mark Abraham wrote: > On 9/05/2011 2:01 PM, Dimitar Pachov wrote: > > Hi, > > On Sat, May 7, 2011 at 9:45 PM, Justin A. Lemkul wrote: > > >> Please clarify - do you wish to maintain the original triclinic >> representation (as -ur tric does) or do you wish to se

[gmx-users] writing trajectory with water molecules within a distance from protein

Dear experts I have a protein simulation in a water box. I now want to write a trajectory containing only the protein, and water molecules within 5 Angstroms of the protein, with the water list being updated each time step. How can one do this? Appreciate the help -- Maria G. Technical Universit

[gmx-users] simulation of a non complete structure

dear users is it rational to do a simulation on a structure witch is not complete? i mean pdb structure doesn't cover whole of the protein but it's active core domain. may be i should be asking this question somewhere else, but i thought some of you may have concerned with such case and in fact i

Re: [gmx-users] simulation of a non complete structure

Sajad Ahrari wrote: dear users is it rational to do a simulation on a structure witch is not complete? i mean pdb structure doesn't cover whole of the protein but it's active core domain. may be i should be asking this question somewhere else, but i thought some of you may have concerned wit

[gmx-users] total force acting on group

Hi dear user's I want to calculate total force acting on one certain atom or group. gromacs dose not have tools for force analysis, and FDA only give pair forces between one group of atoms how can i do this? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

Re: [gmx-users] ambar to opls force field

Nilesh Dhumal wrote: I used g_dipoles to calculate dielectric constant. g_dipoles -f water.trr -s water.tpr -eps Group 0 ( System) has 768 elements Group 1 ( Protein) has 768 elements Group 2 ( Protein-H) has 256 elements Group 3 ( C-alpha) has 0 elem

[gmx-users] git server maintenance finished

Hi, The git server, git.gromacs.org, was moved to a new machine: tcbs03.theophys.kth.se, 130.237.25.132. It may take some time for the DNS to propagate. The old server is still available at git-old.gromacs.org, 130.237.25.210. We'll take it offline after we make sure the new one runs fine.

Re: [gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0

Hi, I recompiled gromacs 4.5.4 and fftw3.2.2 with the newest version off the intel compiler suit 12.0.2, still leading to segmentation faults. As suggested, I tried lots of combinations of different forcefields, water types and *.pdb's. Non of them was successful, so my segmentation fault is repro

[gmx-users] Fatal error: Atomtype CB not found

Dear Sir Greetings! I am following every gromacs applications based on your manuals. I now get stuck in grompp -energy minimization step during generation of .tpr file for my ligand and protein. the error which i found is the following, Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp

Re: [gmx-users] regarding nacl simulation in water using tabulated potentials

i had three tables one for solvent na and solvent cl ions (obeying lj potential) and na ,cl obeying my own potential.i have the following mdp file em.mdp title = nacl cpp = /usr/bin/cpp ; the c preprocessor define= -DEFLEXIBLE integrator = md dt = 0.001 ; ps ! nsteps = 6 nstlist = -1 ns_type =

Re: [gmx-users] Fatal error: Atomtype CB not found

ITHAYARAJA wrote: Dear Sir Greetings! I am following every gromacs applications based on your manuals. I now get stuck in grompp -energy minimization step during generation of .tpr file for my ligand and protein. the error which i found is the following, Ignoring obsolete mdp entry 'titl

[gmx-users] tip4p.itp

Does anybody know the reference for TIP4P water, which is supplied in tip4p.itp in the /share folder, please? -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

Re: [gmx-users] tip4p.itp

On 2011-05-09 20.19, Vitaly Chaban wrote: Does anybody know the reference for TIP4P water, which is supplied in tip4p.itp in the /share folder, please? -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 Do you think it is not the regular on

Re: [gmx-users] tip4p.itp

Vitaly Chaban wrote: Does anybody know the reference for TIP4P water, which is supplied in tip4p.itp in the /share folder, please? Reference 96 in the manual. -Justin -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- ===

Re: [gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0

kalav...@gmx.net wrote: Hi, I recompiled gromacs 4.5.4 and fftw3.2.2 with the newest version off the intel compiler suit 12.0.2, still leading to segmentation faults. As suggested, I tried lots of combinations of different forcefields, water types and *.pdb's. Non of them was successful, so my

[gmx-users] Re: git server maintenance finished

The DNS seems to be finished updating now. Let me know if something doesn't work as expected with the new server. Cheers, Rossen On 5/9/11 5:25 PM, Rossen Apostolov wrote: Hi, The git server, git.gromacs.org, was moved to a new machine: tcbs03.theophys.kth.se, 130.237.25.132. It may take som

[gmx-users] Re: Re: tip4p.itp

> On 2011-05-09 20.19, Vitaly Chaban wrote: > > Does anybody know the reference for TIP4P water, which is supplied > > in tip4p.itp in the /share folder, please? > > > > -- > > Dr. Vitaly V. Chaban, Department of Chemistry > > University of Rochester, Rochester, New York 14627-0216 > > > Do you thi

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

Hi, there is no tool to do that. Trajectories assume to have the same number of atoms per frame. What you can do is use g_order (it gives you the water sorted by distance and the number of water within .5nm) or g_select (it can give you an index file with the atoms within .5nm for each frame) Rol

Res: [gmx-users] different number of waters (grompp)

Ricardo O. S. Soares wrote: > Hello dear users, > > I'm having a problem trying to simulate one trimer. I'm using tip4p water and >right after I fill the box with water and try to pre-process (grompp) the >resulting .gro and .top, I get the following error: > > > -

Re: [gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0

On 10/05/2011 1:38 AM, kalav...@gmx.net wrote: Hi, I recompiled gromacs 4.5.4 and fftw3.2.2 with the newest version off the intel compiler suit 12.0.2, still leading to segmentation faults. As suggested, I tried lots of combinations of different forcefields, water types and *.pdb's. Non of them

Re: [gmx-users] Fatal error: Atomtype CB not found

On 10/05/2011 3:10 AM, Justin A. Lemkul wrote: ITHAYARAJA wrote: Dear Sir Greetings! I am following every gromacs applications based on your manuals. I now get stuck in grompp -energy minimization step during generation of .tpr file for my ligand and protein. the error which i found is th

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

On 10/05/2011 12:50 AM, maria goranovic wrote: Dear experts I have a protein simulation in a water box. I now want to write a trajectory containing only the protein, and water molecules within 5 Angstroms of the protein, with the water list being updated each time step. How can one do this? A

Re: [gmx-users] total force acting on group

On 10/05/2011 12:43 AM, rasool.fakh...@ut.ac.ir wrote: Hi dear user's I want to calculate total force acting on one certain atom or group. gromacs dose not have tools for force analysis, and FDA only give pair forces between one group of atoms how can i do this? nstfout = xx in your .mdp file w

Re: [gmx-users] How to recenter solvent around solute

On 10/05/2011 12:24 AM, Dimitar Pachov wrote: On Mon, May 9, 2011 at 1:39 AM, Mark Abraham > wrote: On 9/05/2011 2:01 PM, Dimitar Pachov wrote: Hi, On Sat, May 7, 2011 at 9:45 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: Please c

Re: [gmx-users] regarding nacl simulation in water using tabulated potentials

On 10/05/2011 2:20 AM, sreelakshmi ramesh wrote: i had three tables one for solvent na and solvent cl ions (obeying lj potential) and na ,cl obeying my own potential.i have the following mdp file em.mdp title = nacl cpp = /usr/bin/cpp ; the c preprocessor define= -DEFLEXIBLE integrator = md dt