[gmx-users] Vacuum Simulation of Alanine Dipeptide =>production run

Hi, to create some toy data I want to do a vacuum simulation of Alanine Dipeptide with Gromacs. For the production run script I used the gmx-user mailing list thread [1a-d], the tutorial [2] and the corresponding sample script [3]. 1a: http://www.gromacs.org/pipermail/gmx-users/2006-August/0232

Re: [gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

Hi Chris, > did you try searching the archives? Yes I tried to search in archive for "No default Ryckaert-Bell. types", but I didn't find anything useful. But I didn't had the idea to search for the string combination: "ACE+NAC+oplsaa" . With the correction of topology file it worked. Thanks

[gmx-users] pull.pdo and AFM force

All users: I want to calculate the AFM force in afm pulling, is there a script to obtain forces from afm pulling! In fact, g_wham can not run, it is very depressed. Please help me! Thank you in advance! - 雅虎邮箱，您的终生邮箱！

[gmx-users] Help - No default Bond types dna

Hello. Ie been trying to run a DNA simulation with gromacs using amber99 force field. I've started with my DNA sequence complexed with the protein, but then decided to separate them to know exactly what the problem was. Now I am not even using the DNA sequence from my pdb file. I`ve used the NAB se

[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

>What do I have to adjust to get rid of the error message? did you try searching the archives? http://www.gromacs.org/pipermail/gmx-users/2006-September/023875.html http://www.gromacs.org/pipermail/gmx-users/2006-September/023872.html Chris. -- original message -- Hi, to create some toy data

[gmx-users] g_rotacf

Hi, I want to clarify a few of the things about the usage of g_rotacf (for rotational correlation function for molecules). In the manual it is given like the following: g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1 -beginfit 2.5 -endfit 20.0 I understood that -f, -s options

Re: [gmx-users] How to display simulation box in VMD?

You should have a look in the archives of the VMD mailing-list... Or check this page: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcbox/ Nicolas Suman Chakrabarty wrote: How do I display the actual simulation box in VMD for a gromacs configuration/trajectory? Is it possible? By

[gmx-users] Re: The WARNING

> > 1. If I have the correct information in my .top file and .gro file, > I could successfully run "GROMPP" command without the warning. > > And, I could ignore the warning from the analysis tools. > right? > If you have got .tpr submit it to the analysis tools. -- Vitaly V. Chaban School of Ch

[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

Hi, to create some toy data I want to do a vacuum simulation of alanine dipeptide with Gromacs. I used charmm ("generate" command) to build the structure of alanine dipeptide. The structure in "charmm notation" is "ACE-ALA-CT3" and in "gromacs notation" is "ACE-ALA-NAC" . The charmm output is a

[gmx-users] How to display simulation box in VMD?

How do I display the actual simulation box in VMD for a gromacs configuration/trajectory? Is it possible? By default it shows only the axes. Regards, Suman Chakrabarty. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/

Re: [gmx-users] rb1 test failed after recompiling gromacs 3.3.2

Justin A. Lemkul wrote: Nicolas Sapay wrote: Nicolas Sapay wrote: Hello, I've run the gmxtest on Gromacs-3.3.2. One simple test failed: Testing rb1 . . . *** glibc detected *** realloc(): invalid next size: 0x082c0180 *** sh: line 1: 27398 Aborted mdrun >mdrun.out 2

[gmx-users] Re: The WARNING

Lin, A .gro file does not have information regarding masses. Therefore, any operation involving masses (mass-weighted fitting) will not be performed optimally. Cheers, Tsjerk On Thu, Aug 21, 2008 at 9:19 PM, Chih-Ying Lin <[EMAIL PROTECTED]> wrote: > Hi > As you described... > This is not a

[gmx-users] The WARNING

Hi As you described... This is not a grompp warning, but a warning from one of the analysis tools. grompp will never take masses 'out of the blue', but will always use the force field description (atom type definitions) or the mass specified in the .top/.itp file. It will bail out if no mass is

Re: [gmx-users] rb1 test failed after recompiling gromacs 3.3.2

Nicolas Sapay wrote: Nicolas Sapay wrote: Hello, I've run the gmxtest on Gromacs-3.3.2. One simple test failed: Testing rb1 . . . *** glibc detected *** realloc(): invalid next size: 0x082c0180 *** sh: line 1: 27398 Aborted mdrun >mdrun.out 2>&1 FAILED. Check file

Re: [gmx-users] rb1 test failed after recompiling gromacs 3.3.2

Nicolas Sapay wrote: Hello, I've run the gmxtest on Gromacs-3.3.2. One simple test failed: Testing rb1 . . . *** glibc detected *** realloc(): invalid next size: 0x082c0180 *** sh: line 1: 27398 Aborted mdrun >mdrun.out 2>&1 FAILED. Check files in rb1 I have more cl

[gmx-users] Re: Salt molecule - ion bond

> The salt R-N(CH3)3-Br. > And, any differences for assigning the Van-der waal and LJ parameters > between salt and organic molecules? no difference. - Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaba

Re: [gmx-users] Salt molecule - ion bond

Chih-Ying Lin wrote: Hi The salt R-N(CH3)3-Br. Could anyone tell me how to assign the force field parameter for the salt molecule ; especially for the ion bond/ ion angle/ There will be no such thing, unless the force field has already assigned it. But since a covalent bond is probably unl

Re: [gmx-users] tfe and gromos9653a

shahrbanoo karbalaee wrote: Dear justin I guess I did right.I add in my topoly file tfe in part of dehedrals " gd_24".(from your edit in dmso topolgy last another mail)and I could minimize. what do you think this adding ?.any way thank you for every thing.now about my peptide I have this e

Re: [gmx-users] regarding 2002 post showing protein unfolding with long timesteps

[EMAIL PROTECTED] wrote: David van der Spoel, can you please comment on this post of your from 2002: "long timesteps combined with dummies give me unfolding proteins while without dummies and 2 fs the systems are stable. These are long-time effects (i.e. after a couple of ns things start to ha

RE: [gmx-users] cgnr

Hi Lin, Please read the manual. By checking the "Index" section you'll find charge group. For example, there is a paragraph in page 20. Lanyuan Lu > Date: Thu, 21 Aug 2008 09:52:35 -0700 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gm

[gmx-users] Salt molecule - ion bond

Hi The salt R-N(CH3)3-Br. Could anyone tell me how to assign the force field parameter for the salt molecule ; especially for the ion bond/ ion angle/ Does there exist "dihedral angle " between the ion Br and R ? And, any differences for assigning the Van-der waal and LJ parameters between salt a

[gmx-users] cgnr

Hi As Justin described, cgnr = charge group number could anyone explain more about this ? and, how to determin cgnr? Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archi

[gmx-users] tfe and gromos9653a

Dear justin I guess I did right.I add in my topoly file tfe in part of dehedrals " gd_24".(from your edit in dmso topolgy last another mail)and I could minimize. what do you think this adding ?.any way thank you for every thing.now about my peptide I have this error .(in c terminal peptide i

[gmx-users] Re: Using Morse potentials with ENCAD force field

It seems because your box should be a bit longer to succeed. Try to enlarge the side (13.2 nm) length. 2008/8/21 Andy Shelley <[EMAIL PROTECTED]>: > No problem the term flattens is porbably not the best technical > description. A better one would be the cnt collapses. > > Andy > > On Thu, Aug 21

[gmx-users] regarding 2002 post showing protein unfolding with long timesteps

David van der Spoel, can you please comment on this post of your from 2002: "long timesteps combined with dummies give me unfolding proteins while without dummies and 2 fs the systems are stable. These are long-time effects (i.e. after a couple of ns things start to happen). I have to do more tes

Re: [gmx-users] simulations backward in time

On Thu, 2008-08-21 at 10:32 -0400, Sumanth Jamadagni wrote: > Using a negative 'dt' in the mdp file does not not seem to cause any > simulation problems (tested on a waterbox- doesn't crash). I am not sure > if the system is evolving backwards in time though. I am not sure how to > check that. S

Re: [gmx-users] Visualizing gromacs result

vivek sharma wrote: Hi, Can anybody tell which visualization tool is better out of vmd/pymol/gopenmol to visualize gromacs result.? - watch long trajectories: VMD (reads xtc) - fancy pictures and short movies: pymol (does not read xtc) gopenmol: I don't know. cheers, jochen Thanks in advan

[gmx-users] [Fwd: WARNING: Found more than 12 triclinic correction vectors, ignoring some.]

Hi all, I tried to send this to the gmx-developers list several hours ago, but it never showed up, so I'll try here. There also appears to be problems with the Admin pages for the mailing lists (I went to check and make sure my subscription to that list was active). I am simulating a simpl

Re: [gmx-users] New Gromacs-CPMD QMMM webpage

Hi Vidhya, You can also find the qmmm_examples in your downloaded gromacs source code: gmx-3.3.1_qmmm-1.3.2. location: gmx-3.3.1_qmmm-1.3.2/share/qmmm_examples You will find the templates of 'CPMD_inp.tmpl' and 'runcpmd' there in the examples. However, all the runcpmd templates seem to be for

[gmx-users] simulations backward in time

Using a negative 'dt' in the mdp file does not not seem to cause any simulation problems (tested on a waterbox- doesn't crash). I am not sure if the system is evolving backwards in time though. I am not sure how to check that. But I think, all I require is that the equations of motion be integr

Re: [gmx-users] Re: Simulations backward in time

Yes. Namely at the very step the velocities should be inverted to invert a time flow. My remark was addressed namely to the word "initial". 2008/8/21 Berk Hess <[EMAIL PROTECTED]>: > Surely inverting the velocities changes the direction of the system > evolution. > The state of the system is giv

FW: [gmx-users] Re: Simulations backward in time

From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: RE: [gmx-users] Re: Simulations backward in time Date: Thu, 21 Aug 2008 16:11:56 +0200 Surely inverting the velocities changes the direction of the system evolution. The state of the system is given by x and v. The evolution is deter

[gmx-users] Re: Simulations backward in time

> > > Vitaly Chaban wrote: >>> I wanted to perform some simulations backward and forward in time (for >>> transition path sampling ). If I specify a negative value for 'dt' in the >>> mdp file, would that work for backward integration of the equations of >>> motion ? >> >> Time does not run back.

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 89

> Hi, > Can anybody tell which visualization tool is better out of > vmd/pymol/gopenmol to visualize gromacs result.? > > Thanks in advance, > Vivek I am a fan of VMD. But for quick looking at the trajectory ngmx is a bit more convenient. -- Vitaly V. Chaban School of Chemistry National Univers

Re: [gmx-users] Re: Simulations backward in time

In conf.gro? It will change only the first steps but will not change the direction of the system evolution. As I understand, the topicstarter wanted to perform the simulation "backwards"... Vitaly 2008/8/21 Jochen Hub <[EMAIL PROTECTED]>: > Vitaly Chaban wrote: >>> >>> I wanted to perform some

Re: [gmx-users] HELP::Running Gromacs in parellel

vivek sharma wrote: Hi There, I am running gromacs on parellel system using the submit command. Commands are running fine, but the .trr file I got is not matching with the trr file I got while running command in serial. Based on what analysis? Have you done gmxcheck -f1 -f2 on these .trr

[gmx-users] Visualizing gromacs result

Hi, Can anybody tell which visualization tool is better out of vmd/pymol/gopenmol to visualize gromacs result.? Thanks in advance, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search t

Re: [gmx-users] Re: Simulations backward in time

Vitaly Chaban wrote: I wanted to perform some simulations backward and forward in time (for transition path sampling ). If I specify a negative value for 'dt' in the mdp file, would that work for backward integration of the equations of motion ? You could also invert the initial velocitie

[gmx-users] Re: New Gromacs-CPMD QMMM webpage

>>  >> dear sir, >>            i am vidhya sankar speaking . i am not able to down >> load QM/MM exampiles files since it take much time and huge memory (156Mb) >> often net is disconnected >> could you please send some example input files of CPMD part mainly >> 'CPMD_inp.tmpl'Â

[gmx-users] Re: Using Morse potentials with ENCAD force field

> > Actually I think I am using the gromos force field. I have been using > Christopher Stiles page as a guide to get started with using CNT > http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications were > made to ffgmx files. So I believe I am using the gromos forcefield. Is the >

[gmx-users] HELP::Running Gromacs in parellel

Hi There, I am running gromacs on parellel system using the submit command. Commands are running fine, but the .trr file I got is not matching with the trr file I got while running command in serial. Also, I am getting a number of log files(equal to number of nodes I am choosing). How should I ana

[gmx-users] simulation problems

Hello gmx users I am simulating a system composed of of an organic molecule (a 10 -CH=CH- thread with polyciclyc ends) in CH3CN. The system is made up of 6000 atoms in a cubic box. I am using the gromos the 96 force field. The solute molecule is elongated like : A-B where A and B are the

Re: [gmx-users] tfe

shahrbanoo karbalaee wrote: Dear justin for have tfe30% after I got tfedrg.top with pdb2gmx and force field gromos965a. I do t this command : editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro genbox -cp box.gro -cs spc216.gro ci tfedrg.gro - nmol 40 -p topol.top -o solvated.gro I

[gmx-users] tfe

Dear justin for have tfe30% after I got tfedrg.top with pdb2gmx and force field gromos965a. I do t this command : editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro genbox -cp box.gro -cs spc216.gro ci tfedrg.gro - nmol 40 -p topol.top -o solvated.gro I did that command with spc.gro(I

Re: [gmx-users] Re: Simulations backward in time

Vitaly Chaban wrote: I wanted to perform some simulations backward and forward in time (for transition path sampling ). If I specify a negative value for 'dt' in the mdp file, would that work for backward integration of the equations of motion ? Time does not run back. :) It's a bad idea. I t

[gmx-users] Re: Simulations backward in time

> I wanted to perform some simulations backward and forward in time (for > transition path sampling ). If I specify a negative value for 'dt' in the > mdp file, would that work for backward integration of the equations of > motion ? Time does not run back. :) It's a bad idea. -- Vitaly V. Chaba

Re: [gmx-users] Re: The WARNING

Tsjerk, probably you are right about grompp. I thought the user had received this warning when preparing a system. Like genbox and so on... So, I mean maybe he had not .tpr at that moment... Vitaly 2008/8/21 Tsjerk Wassenaar <[EMAIL PROTECTED]>: > Vitaly, > > This is not a grompp warning, but a w

Re: [gmx-users] Re: The WARNING

Vitaly, This is not a grompp warning, but a warning from one of the analysis tools. grompp will never take masses 'out of the blue', but will always use the force field description (atom type definitions) or the mass specified in the .top/.itp file. It will bail out if no mass is properly defined

Re: [gmx-users] pdb file ???

Hi Lin, If you include bromide, you won't have excess charge... So, no need for adding more counterions. Cheers, Tsjerk On Thu, Aug 21, 2008 at 8:20 AM, Chih-Ying Lin <[EMAIL PROTECTED]> wrote: > Hi > It is the water-molecule system. > For a molecule, like R-N(CH3)3-Br, I could make a pdb fil

[gmx-users] Re: tfe.itp

> after edit tfe.itp , I did the command grompp and I got this error : > error input solvated.gro. Do I have to make spc.gro with tis > forcefield(gromos965a)? > No solvated.gro? Access rights? dos format? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.

[gmx-users] RE: [ atomtypes ] are not case sensitive?

Well, I didn't developed Amber FF neither GAFF and although only Amber FF is ported to GMX, one of the greatest appealing of Amber is its antechamber and GAFF for generating topology for non usual compounds. Looking at the way GAFF was developed (remember G is for generalised) is seemed a natural

[gmx-users] Re: The WARNING

> WARNING: masses will be determined based on residue and atom names, > this can deviate from the real mass of the atom type > > Is this warning serious? > Could any one tell me how to fix the warning? > I see nothing wrong with my .top and my .gro file. > You should have right masses in y

[gmx-users] call for help

Hello, everyone, I meet a problem when I perform the gromacs. I fixed two C60 molecule at a certain distance(2.02 nm) by SHAKE algorithm. The atoms have no charge on them. So the interaction between the molecules should be the van der Waals interactions. I set the van der Waals cut off to be 1.2n