Re: [gmx-users] Re: mdrun on GROMACS 3.3.1

Hi Sheeba, with time I understood why it was happening. Check in the mdp file if you still have the parameters to couple with the coarse grained file and comment them. If they are present in the mdp file then mdrun looks for the coarse grained file. Hope this will be helpful Francesca 2012/8

Re: [gmx-users] problem in making a trajectory

h for your help Francesca 2012/6/16 Justin A. Lemkul > > > On 6/16/12 7:54 AM, francesca vitalini wrote: > >> yes and I do. >> By the way the version of GROMACS I'm using is the 3.3.1, I forgot to >> specify >> that before. >> >> > OK, I

Re: [gmx-users] problem in making a trajectory

yes and I do. By the way the version of GROMACS I'm using is the 3.3.1, I forgot to specify that before. 2012/6/16 Justin A. Lemkul > > > On 6/16/12 7:41 AM, francesca vitalini wrote: > >> Dear Justin, >> >> this is my trjcat command >> >> /home

Re: [gmx-users] problem in making a trajectory

have each structure at a different time step. If I was using it wrongly please correct me. Thanks in advance for all the help. Francesca 2012/6/16 Justin A. Lemkul > > > On 6/16/12 6:48 AM, francesca vitalini wrote: > >> Dear Gromacs Users, >> >> While making a

[gmx-users] problem in making a trajectory

Dear Gromacs Users, While making a trajectory connecting different gro files I got the following output which I don't understand. Continue writing frames from /home/cocktail2/vitalini/reverse_transformation_vacuum/300-166-160/300-166-160_annealing.gro t=1 ps, frame=0 Last frame 0 time

[gmx-users] Re: One molculetype for 3 proteins

if you create a bond you need to have angle, tortion etc... Maybe when you processed pb2gmx it create a bond between the 799 and 801. Francesca -- View this message in context: http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997773.html Sent from the GROMACS Users

[gmx-users] Re: One molculetype for 3 proteins

can you write the atoms 6002 6004 6006 6017 6021 and all informations in your topology file about these atoms?? Francesca -- View this message in context: http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997758.html Sent from the GROMACS Users Forum mailing list

[gmx-users] Re: One molculetype for 3 proteins

I checked and the resul is the same...but now I know I can use -chainsep interactive! -- View this message in context: http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997739.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mail

[gmx-users] Re: One molculetype for 3 proteins

ctory. I used that method and I could apply the distance restraints. Cheers, Francesca -- View this message in context: http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997736.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users ma

[gmx-users] g_mdmat

s, and the area of interest is plotted through xpm2eps only in the lower left corner. How can I manage to obtain a plot that only focuses on the residues provided by the index file? I have been searching the mailing list but couldn't find an answer to that. Thank you in advance. Best -- Fra

Re: [gmx-users] Not able to continue with Equilibration

ntal importance. Unfortunately I couldn't find any more detailed documentation about it. Could anyone explain to me what it does or point me to where to find the related documentation? Thank you very much Francesca 2012/3/30 Mark Abraham : > On 30/03/2012 8:39 AM, francesca vitalini wrote: >>

Re: [gmx-users] Not able to continue with Equilibration

, rcoulomb and rvdw to 1. Any ideas on a faster way to add my position restraints or how to solve the LINCS error? Thank you very much. Francesca 2012/3/29 Justin A. Lemkul : > > > francesca vitalini wrote: >> >> My minimization was done without any constraints. I'm start

Re: [gmx-users] Not able to continue with Equilibration

actly the reason I'm running the nvt equilibration? Or am I misunderstanding something? Thanks Francesca 2012/3/29 : > I didn't follow this whole thread, but I sometimes need to turn off all > constraints when doing minimization. In fact, for that reason I entirely > stop

Re: [gmx-users] Not able to continue with Equilibration

destroied. Am I using some strange parameters for nvt without realizing it? I've started from the mdp file provided by the lysozyme tutorial non the Gromacs webpage. if anyone has any ideas it is more than welcome. Francesca integrator = md; leap-frog integrator n

Re: [gmx-users] Not able to continue with Equilibration

in a cluster or in a strange position. I have added dihedral restraints on them but still the same type of error. I'm using GROMACS 3.3.1. I have tried to switch to a newer version of GROMACS but still the same error. Does anyone have any suggestions? Thanks Francesca MINIMIZATION OUTPUT Steepes

Re: [gmx-users] Generation of the Distance Restraints

I think you can make an index file using make_ndx where you specify the atoms you want to restraint. Hope this can help. Francesca 2012/3/12 James Starlight : > Dear Gromacs users! > > > I want to perform constrained MD simulation of my protein with inclusion of > some experime

Re: [gmx-users] About martini

Either you develop your own version of the mapping or I guess you have to use the old version...sorry, but I'm struggling with it right now and I understand that it can be quite problematic. Francesca 2012/3/9 rama david : > Dear GROMACS specialists, >   How to convert C

[gmx-users] reverse transformation with dihedral restraints

va_random.gro Could it be that the error arises from the fact that the dihedral restraints were calculated from the pdb while the topology was built through pdb2gmx with the flag -missing? I'm looking at CA C N CA dihedrals, could any of those atoms be missing? Thanks Francesca -- gmx-users

Re: [gmx-users] using g_angle

obtain 2 values more than the input number of quadruplets and I don't understand why. Is it here something I'm missing from how it works? Thanks for any help. Francesca 2012/2/29 francesca vitalini : > Thank you. It worked now. > Best > Francesca > > > > 2012/2/29 Mark Ab

Re: [gmx-users] using g_angle

Thank you. It worked now. Best Francesca 2012/2/29 Mark Abraham : > On 1/03/2012 1:00 AM, francesca vitalini wrote: >> >> Hi Mark, >> Thanks for your answer. What I'm trying to do is calculate the value >> in degrees of  the angles listed in my index file

Re: [gmx-users] using g_angle

. Is there a faster way to get a file that has like two columns, one for the dihedral and another one for the angles? Thanks Francesca 2012/2/29 Mark Abraham : > On 29/02/2012 11:54 PM, francesca vitalini wrote: >> >> 2012/2/29 Mark Abraham: >>> >>> On 29/02/201

Re: [gmx-users] using g_angle

2012/2/29 Mark Abraham : > On 29/02/2012 9:39 PM, francesca vitalini wrote: >> >> Hi all, >> I'm trying to use g_angle to calculate a list of dihedrals that I have >> into an hand made index file (angles.ndx), which looks like >> [ dihedrals ] >> 2 5

[gmx-users] using g_angle

nt is instead to know the value in degrees of each angle in the ndx file. Do you have any suggestions apart from building an index file for each angle? Thanks Francesca -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] dihedral

#x27;m doing it correctly or how can I check it by my self? Thanks Francesca -- 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] Calculate Dihedrals

r me as it calculates dihedrals in a different way from the tool g_dihfix for which I need this values. Any idea? Thanks Francesca -- 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/Mai

Re: [gmx-users] mdrun on GROMACS 3.3.1

a lot 2012/1/31 Justin A. Lemkul : > > > francesca vitalini wrote: >> >> Well I'm keeping struggling with this script. Apparently the problem in in >> using the integrator md with the GOMACS 3.3.1 version. In fact the same .mdp >> file with integrator steep works. w

Re: [gmx-users] problems with martinize.py

nks a lot 2012/2/20 Dommert Florian : > On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote: >> Just  one last question Tsjerk, I was trying to load the cg.gro file >> obtained with martinize in vmd and the program says it is unable to >> load the molecule. the resu

Re: [gmx-users] problems with martinize.py

90.00 P 1 1 ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00 ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00 ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00 TER ENDMDL Does it sound right to you? Thanks 2012/2/20 francesca vitalini

Re: [gmx-users] problems with martinize.py

rough the pdb. Do you know a fastest way to make it work? Thanks However, my Martini account never worked, don't know why, so I cannot post it directly. 2012/2/20 Tsjerk Wassenaar : > Hey Francesca, > > Now there's a small bug in the program. Sorry about it. We'll put th

Re: [gmx-users] problems with martinize.py

GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 TER can you please explain which the problem is to me? thanks 2012/2/20 Tsjerk Wassenaar : > Hi Frances

Re: [gmx-users] problems with martinize.py

8]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' 2012/2/20 Tsjerk Wassenaar : > Hi Francesca, > > The problem is that the second line of your gro file indicates there > are 2410 atoms in the file, while there are only 25. Did you manually

Re: [gmx-users] problems with martinize.py

2.91477 2.91477 Can you help me on that? Thanks 2012/2/20 Tsjerk Wassenaar : > Hi Francesca, > > Is this the latest version > (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)? > If it is, please send me the input file and I'll fix the bug. Note &

[gmx-users] problems with martinize.py

for int() with base 10: '2.' Can anyone help me on that? Thanks -- Francesca -- 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! P

Re: [gmx-users] getting dssp executable

Thanks. I was mislead by the syntax in the online reference and forgot to change everything into bash scripting. You have been very very helpful! 2012/2/17 Justin A. Lemkul : > > > francesca vitalini wrote: >> >> export DSSP /home/cocktail/vitalini/gromacs_special/bin/dssp

Re: [gmx-users] getting dssp executable

export DSSP /home/cocktail/vitalini/gromacs_special/bin/dssp 2012/2/17 Justin A. Lemkul : > > > francesca vitalini wrote: >> >> Thanks! >> However now I jet another error >> -bash: export: `/home/cocktail/vitalini/gromacs_special/bin/dssp': not >> a

Re: [gmx-users] getting dssp executable

h the binary file to make it work? n the dssp website they don't write anything about it. Thanks again 2012/2/17 Justin A. Lemkul : > > > francesca vitalini wrote: >> >> Dear all, >> In order to get the secondary structure of my pdb file I need to run >> the do

[gmx-users] getting dssp executable

message: -bash: setenv: command not found Any help? Thanks -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49

[gmx-users] NME not found in rtp

that, any help? Otherwise, I'm actually just looking for a toy system with which just play around as I'm having issues with the reverse transformation. Any suggestion for a pdb? thanks! -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathem

Re: [gmx-users] problems with pdb2gmx gromacs 3.3.1 version

012/2/17 Mark Abraham : > On 17/02/2012 9:14 PM, francesca vitalini wrote: >> >> I tried, but apparently the atom that it is looking for exist already >> in the rtp file!! >> >> this is the error >> >> Program pdb2gmx, VERSION 3.3.1 >> Source code f

Re: [gmx-users] problems with pdb2gmx gromacs 3.3.1 version

[ dihedrals ] -CA -C N H1 gd_14 [ impropers ] -C -O N -CA gi_1 N H H -C gi_1 Any help? 2012/2/16 Justin A. Lemkul : > > > francesca vitalini wrote: >> >> Do you mean that I can just use the new version of pdb2gmx than change >> the included forcefield

[gmx-users] reverse transformation

sing the GROMACS 3.3.1 version of pdb2gmx I get the aa.top Trying to reconvert from cg to aa I obtain the message pasted before. Any ideas? -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berli

Re: [gmx-users] problems with pdb2gmx gromacs 3.3.1 version

Do you mean that I can just use the new version of pdb2gmx than change the included forcefield and in case the name of the atoms and it should work? 2012/2/16 Justin A. Lemkul : > > > francesca vitalini wrote: >> >> Hi all! >> I'm trying to create a topology fil

[gmx-users] problems with pdb2gmx gromacs 3.3.1 version

ry with 3 atoms while sorting atoms --- Any suggestions? Thanks -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zed

Re: [gmx-users] Energy minimization Error

exactly when Open MPI kills them. So... How ca I overcome the issue of overlapping atoms? Thanks Fra 2012/2/10 francesca vitalini > In fact in the reverse transformation I'm feeding the CG structure > information. > Once I look through VMD to the FG structure I notice that the back

Re: [gmx-users] Energy minimization Error

;t think I need more than energy minimization for that. What do you think? 2012/2/10 Mark Abraham > On 11/02/2012 12:41 AM, francesca vitalini wrote: > > In order to overcome the problem I tried to fix everything except the > backbone (solvent, sidechain and CA, as I want the struct

Re: [gmx-users] Energy minimization Error

ibrated it yet and I'm keeping it fixed which could also be a source of overlapping. Any ideas? Thanks. Francesca 2012/2/10 Justin A. Lemkul > > > francesca vitalini wrote: > >> I achieve >> >> Steepest Descents converged to machine precision in 205 steps,

Re: [gmx-users] Energy minimization Error

5496e+07 Maximum force = 2.0486184e+12 on atom 4479 Norm of force = 7.2424045e+13 but again the same issue with table extent and still the production of pdb files. Any explanations? Thanks Francesca 2012/2/9 Justin A. Lemkul > > > francesca vitalini wrote: > >>

Re: [gmx-users] Energy minimization Error

Tryed the double precision without any success... Again the same type of error message. Might need to try other minimization algorithm. Any suggestions on that? 2012/2/9 Justin A. Lemkul > > > francesca vitalini wrote: > >> Hi all! >> I'm trying to run some ene

[gmx-users] Energy minimization Error

000 152461 1000 1000 1000 152471 1000 1000 1000 152481 1000 1000 1000 152491 1000 1000 1000 152501 1000 1000 1000 152511 1000 1000 1000 .. 187

[gmx-users] harmonic distance restraints

aints ] specified with type 6. However I cannot find the command to generate this .itp . On the contrary, for positions restraints there is the genpr command that does it, so I'm looking for the equivalent for the distance restrains. Can anyone help? Btw, I'm using GROMACS 3.3.1, Thanks Francesc

Re: [gmx-users] trjconv select group

gt; On 4/02/2012 12:56 AM, francesca vitalini wrote: >> >> Yes but those tips are not for bash scripts... :( > > You asked how to make the script always use the same no-longer-interactive > selection. That's the information on the page we linked. The bash loop glue >

Re: [gmx-users] trjconv select group

ina > On Friday 03,February,2012 09:56 PM, francesca vitalini wrote: > >> Yes but those tips are not for bash scripts... :( >> > > You'd better post what you have done so far about this script, > > probably someone can help you improve or refine it

Re: [gmx-users] trjconv select group

Yes but those tips are not for bash scripts... :( 2012/2/3 Mark Abraham > On 4/02/2012 12:21 AM, francesca vitalini wrote: > >> Hi! >> I have to use the gromacs command trjconv to obtain a .gro file from a >> .xtc and a .pdb file. I have to do it for several files in a

[gmx-users] trjconv select group

tips? Thanks Francesca -- 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't post (un)subscribe requests to the list. Use the www interfa

Re: [gmx-users] mdrun on GROMACS 3.3.1

mtype CH2R not found any suggestions here? Thanks Francesca 2012/1/31 Francesca Vitalini > Thank you Justin for your quick reply. Unfortunately I cannot use a more > modern version of GROMACS as my topology and .gro files where first created > for a reverse transformation from cg

Re: [gmx-users] mdrun on GROMACS 3.3.1

n) Loaded with Money WARNING: Incomplete frame: nr 0 time 0 Segmentation fault I have checked with gmxcheck the .trr input file as it was suggested in another discussion, and apparently it is ok, so I really don't know what to do. Can you help me with that? Thanks Francesca Il giorno 31/gen/2012,

Re: [gmx-users] mdrun on GROMACS 3.3.1

Actually the directory is of my own and I have created it in my home directory so that shouldn't be a problem as I also have created other files in the same directory without any problems so far. Other ideas? Thanks Francesca Il giorno 31/gen/2012, alle ore 13.02, Justin A. Lemkul ha sc

[gmx-users] reverse transformation

. So I was wondering if the ions are mapped in the fg_w.itp files and how or if there is an appropriate .itp file for mapping the ions from cg to fg. Thanks Francesca -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

[gmx-users] GROMACS_reverse version command g_fg2cg

ns Cleaning up temporary file gromppqBsIeH --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 758 Fatal error: Atoms in the .top are not numbered consecutively from 1 Hope you can help me with that. Many Thanks Francesca -- gmx-users

[gmx-users] GROMACS_reverse version command g_fg2cg

ns Cleaning up temporary file gromppqBsIeH --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 758 Fatal error: Atoms in the .top are not numbered consecutively from 1 Hope you can help me with that. Many Thanks Francesca -- gmx-users

[gmx-users] Voronoi tessellation

nd of atoms? I need to check the xy coordinates of these atoms from the average structure or for each picosecond? If someone can explain me this analysis I'll appreciate, in alternative, could you suggest me a good article able to help me with this analyses? Thanx, Francesca -- gmx-use

[gmx-users] (no subject)

substitution of these atoms? Because I can try  to add the parameters in the five coloumns present but I should know if these values are right. thanks, francesca -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the a

[gmx-users] OPLS implicit solvent problems

267= Co in COOH opls_268= Oh in COOH opls_269= Oc in COOH neutral opls_270= H in COOH in the file gbsa.itp in opls.ff directory these atoms missing. Now, have I done something wrong? If is all ok, is it possible to create these missin