Re: [gmx-users] adding SR2++ to charm27 force field

Dear Mark and Justin, Hi, Justin, I share the files in the dropbox to you. Thanks. Here is the output: tm@tm-HP-Z420-Workstation:~/bmp2$ grompp -f ions.mdp -c pb.pdb -p topol.top -o ions.tpr GROMACS:gmx grompp, VERSION 5.0.4 GROMACS is written by: Emile Apol Rossen Apostolov Herm

[gmx-users] making bilayers including a lipid-like molecule

Dear Gromacs users, I was wondering how can I make initial structures for bilayers, micells and liposomes composed of different lipids including some lipid-like molecules. I am interested in different mixing ratios in two leaflets in bilayer and liposome cases. I have the coordinate and topology

Re: [gmx-users] pi stacking

A recent publication by Brown et. al. which appears in the latest issue of JCTC may also be relevant. See the title below "Stacking free energies of all DNA and RNA nucleoside pairs and dinucleoside-monophosphates computed using recently revised AMBER parameters and compared with experiment " O

Re: [gmx-users] trjcat with settime option using command line

On 4/15/15 10:33 AM, Rebeca García Fandiño wrote: Dear GROMACS users, I am trying to concatenate several trajectories with identical times using the command trjcat with the options -cat and -settime. I have to introduce manually the option "c" each time a new trajectory is read. I would like to

Re: [gmx-users] pi stacking

On 4/15/15 10:28 AM, soumadwip ghosh wrote: Dear Tushar, I dint get what you mean by 'effect of salt concentration can not be simulated in GROMACS'. I am simulating a single stranded DNA which is negatively charged in its native state and the added salt is bound to affect i

Re: [gmx-users] Fe2+ non bonded parameters for AMBER

On 4/15/15 10:21 AM, Raj D wrote: Dear Jastin, Exactly, I would like to study few important mutants which falls well out of Fe2+ coordinating shell and the study is about to compare dynamics of the wild type and mutant systems and I hoping a stable simulation with a crude approximation of acti

Re: [gmx-users] Clusters

I have a script teste.sh which contains: #!/bin/bash #$ -S /bin/bash #PBS -l nodes=8:ppn=6 source /home/dadalt/gmx-5.0.4/bin/ grompp -f md.mdp -c 1UBQ_400_npt.gro -t 1UBQ_400_npt.cpt -p topol.top -o product.tpr /usr/lib64/openmpi/bin/mpirun -np 8 mdrun_mpi -v -deffnm product I use the

Re: [gmx-users] Mdrun and minimum image convention

Hi Catarina, I have an MD wrapper that comprises a monitoring mechanism, which allows terminating a simulation after a certain condition is met. Of course, such a mechanism interferes with the MD process, but it will usually add just a bit every so many minutes, checking the results at intervals.

Re: [gmx-users] Mdrun and minimum image convention

Hi, Probably not, unless there's lots of people who'd find it useful. You do have the option of stopping mdrun periodically and scripting a call to gmx mindist on the final frame to see if a problem was likely to have occurred over the trajectory. This would be more efficiently performed during th

Re: [gmx-users] Topology file for Fullerene with OPLS_AA force field

it's very much similar creating topology for CNT using g_x2top. You can search mailing list for that. Recently I have published a paper on fullerene water systems. http://www.tandfonline.com/doi/abs/10.1080/08927022.2014.998212#.VTKritzF8wA if you any problem you can contact me. Thanks Abhijit

Re: [gmx-users] Topology file for Fullerene with OPLS_AA force field

For fullerenes, follow http://www.webcitation.org/66u2xJJ3O and use x2top to build the topology based on OPLSAA. Alex On Wed, Apr 15, 2015 at 12:51 AM, saeed poorasad wrote: > Hi Gromacs users , > I want to have a system with one C60 and about 1000 water molecules .I > tried to use pdb2gmx on

Re: [gmx-users] GMX 5.0.4 gmx gangle to choose the normal vector of a plane

Dear Mark, >>Can't you get the angle you want by subtracting the one you have from 90? I've tried to solve by add 90, but I found that sometimes it's adding 90, sometimes it's subtracting, depending on the positions of the two planes? Xujun From: gromacs.o

Re: [gmx-users] How can I determine how Gromacs was compiled?

On Wed, Apr 15, 2015 at 7:32 PM, Mirco Wahab wrote: > On 15.04.2015 18:41, Andrew DeYoung wrote: >> >> Hi, >> >> I'm running Gromacs 4.5.5. Is there a way to determine how Gromacs was >> compiled on my system? I would like to know whether the person who >> compiled Gromacs used gcc or icc (both

Re: [gmx-users] How can I determine how Gromacs was compiled?

Hi, With version 4.5 extracting the some of information you want is a bit tricky. Note that starting with GROMACS 4.6 all you need is present in the "-version" output of any GROMACS tool including compiler version(s), flags used, options enabled at compilation, etc. With v4.5 this information is

Re: [gmx-users] How can I determine how Gromacs was compiled?

On 15.04.2015 18:41, Andrew DeYoung wrote: Hi, I'm running Gromacs 4.5.5. Is there a way to determine how Gromacs was compiled on my system? I would like to know whether the person who compiled Gromacs used gcc or icc (both compilers are available and were presumably available when the compila

[gmx-users] How can I determine how Gromacs was compiled?

Hi, I'm running Gromacs 4.5.5. Is there a way to determine how Gromacs was compiled on my system? I would like to know whether the person who compiled Gromacs used gcc or icc (both compilers are available and were presumably available when the compilation occurred) and, if possible, what version

Re: [gmx-users] Mdrun and minimum image convention

Thank you for the clarification Mark. Would you consider to add such feature (as an mdrun flag for example: -pi ) in the next GROMACS versions? On 15 April 2015 at 17:12, Mark Abraham wrote: > Hi, > On 15/04/2015 3:55 pm, "Catarina A. Carvalheda dos Santos" < > c.a.c.dossan...@dundee.ac.uk> wro

Re: [gmx-users] GMX 5.0.4 gmx gangle to choose the normal vector of a plane

Hi, Can't you get the angle you want by subtracting the one you have from 90? Mark On 15/04/2015 5:58 pm, "LIANG Xujun" wrote: > Dear GROMACS users, > > I am now using gromacs 5.0.4 to calculate the angle between the normal > vector of a plane 1 and the COM (center of mass) vector of plane 1 an

Re: [gmx-users] Mdrun and minimum image convention

Hi, On 15/04/2015 3:55 pm, "Catarina A. Carvalheda dos Santos" < c.a.c.dossan...@dundee.ac.uk> wrote: > > Hi there, > > Is there any way to control the minimum distance with periodic images > during mdrun and exit the simulation automatically if this distance is > equal or lower than the user-defin

[gmx-users] GMX 5.0.4 gmx gangle to choose the normal vector of a plane

Dear GROMACS users, I am now using gromacs 5.0.4 to calculate the angle between the normal vector of a plane 1 and the COM (center of mass) vector of plane 1 and plane 2, I used the following command: gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 plane -group1 plane 1 (I tried to use this command

Re: [gmx-users] adding SR2++ to charm27 force field

I asked to see the output. You can't be helped without someone seeing that. Mark On 15/04/2015 3:12 pm, "Ming Tang" wrote: > Hi Mark， > > pdb2gmx doesn't work， and it reminds the same error. Topol file was simply > modified by mean from the topol file generated when considering MG2++ > > Thanks

[gmx-users] trjcat with settime option using command line

Dear GROMACS users, I am trying to concatenate several trajectories with identical times using the command trjcat with the options -cat and -settime. I have to introduce manually the option "c" each time a new trajectory is read. I would like to introduce this line into a script, in such way I

Re: [gmx-users] pi stacking

Dear Tushar, I dint get what you mean by 'effect of salt concentration can not be simulated in GROMACS'. I am simulating a single stranded DNA which is negatively charged in its native state and the added salt is bound to affect its dynamics. This is of course valid if the force

[gmx-users] entropy calculation

Hi Prof. David van der Spoel and Dr. Lemkul, We had quite an interesting discussion related to the entropy calculation in gromacs-4.5 version. Lately, I resumed the configurational entropy calculations in the newer (not latest) version of gromacs. Presently, I am looking into the results of a pa

Re: [gmx-users] Fe2+ non bonded parameters for AMBER

Dear Jastin, Exactly, I would like to study few important mutants which falls well out of Fe2+ coordinating shell and the study is about to compare dynamics of the wild type and mutant systems and I hoping a stable simulation with a crude approximation of active is enough for this purpose because

[gmx-users] Mdrun and minimum image convention

Hi there, Is there any way to control the minimum distance with periodic images during mdrun and exit the simulation automatically if this distance is equal or lower than the user-defined cutoff? I know that this can be monitored with g_mindist, but doing it automatically would avoid wasting simul

Re: [gmx-users] adding SR2++ to charm27 force field

On 4/15/15 9:11 AM, Ming Tang wrote: Hi Mark， pdb2gmx doesn't work， and it reminds the same error. Topol file was simply modified by mean from the topol file generated when considering MG2++ We need to see the *actual terminal output* to diagnose this. It would also be useful if you can

Re: [gmx-users] Fe2+ non bonded parameters for AMBER

On 4/15/15 8:37 AM, Nataraj Balakrishnan wrote: Dear Justin, Thanks for your reply. I just came across one article which uses Fe2+ ion in the active site and as you mentioned they have used phorpherin structure to mimic the Fe2+ parameterzation but nothing mentioned explecitily other parameters

Re: [gmx-users] adding SR2++ to charm27 force field

Hi Mark， pdb2gmx doesn't work， and it reminds the same error. Topol file was simply modified by mean from the topol file generated when considering MG2++ Thanks Sent from my Huawei Mobile Mark Abraham wrote: Thanks. What is the whole pdb2gmx terminal output? Mark On Wed, Apr 15, 2015 at 3:

Re: [gmx-users] error while executing do_dssp program

Hi, With Gromacs version 5.0.4 I get the same error message as Nizar. However, with version 4.6.5 everything works fine. So there may be a bug in the new version. Kind regards, Sam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GM

Re: [gmx-users] Fe2+ non bonded parameters for AMBER

Dear Justin, Thanks for your reply. I just came across one article which uses Fe2+ ion in the active site and as you mentioned they have used phorpherin structure to mimic the Fe2+ parameterzation but nothing mentioned explecitily other parameters details. They have used Amber molecular suit for th

Re: [gmx-users] Pi stacking

On 4/15/15 6:43 AM, Tushar Ranjan Moharana wrote: Hi Soumadwip, Did you see any difference at different salt concentrations? I doubt whether GROMACS can consider salt concentration. Just adding NA and CL doesn't produce the effect of salt concentration in GROMACS. If anybody think I am wrong a

Re: [gmx-users] Pi stacking

On 4/15/15 3:46 AM, Debayan Chakraborty wrote: As far as I know, AMBER force-fields tend to overestimate the stacking interactions in nucleic acids, whereas CHARMM tends to understabilize them. Over all of the ideal stacked base conformations, this is generally true, but the magnitude of the

Re: [gmx-users] how to make average hbond plot in gromacs using xmgrace

On 4/15/15 4:07 AM, rajan kumar wrote: Dear all, i am trying to reduce the variation in the h-bond plot in xmgrace. can we reduce it and how? Probably what you want is the running average feature (in Data->Transformations). -Justin -- == Ju

Re: [gmx-users] Topology file for Fullerene with OPLS_AA force field

As Justin mentioned in an earlier response you aren't going to be able to use pdb2gmx for this, instead you are going to need to use x2top if you are going to build your own topology. Alternatively, you may have better luck building one by hand (see the gromacs manual, and be prepared to spend a

Re: [gmx-users] Fe2+ non bonded parameters for AMBER

On 4/15/15 12:19 AM, Raj D wrote: Dear Users, Had anybody used Fe2+ ions in the active site of protein. I am planning to use one using amber99sb forcefield...please suggest to use the nonbonded parameters for Fe2+ ions, sigma and epsilon values. Most force field parameters are specifically fo

Re: [gmx-users] adding SR2++ to charm27 force field

Thanks. What is the whole pdb2gmx terminal output? Mark On Wed, Apr 15, 2015 at 3:05 AM, Ming Tang wrote: > Dear Justin and mark, > > I modified the files like this: > > aminoacids.rtp > > [ MG ] > [ atoms ] > MG MG 2.000 > [ SR ] > [ atoms ] > SR SR 2.

Re: [gmx-users] problem with dihedral restraints in gromacs 5.0.4

On Wed, Apr 15, 2015 at 4:39 AM, Agnieszka Slowicka wrote: > > > > > > On 4/10/15 12:06 PM, Agnieszka Slowicka wrote: > >> Hello, > >> I have a problem with implementation of dihedral restraints in gromacs > 5.0.4. > >> I introduced restraints into a topology file after the section with > protein

Re: [gmx-users] Pi stacking

Thank you Debayan for your prompt reply. I think now I can conclude that although classical force fields cannot probe pi-pi stacking directly, the non-bonded Coulomb and VDW Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-U

[gmx-users] Virtual sites and diffusion coefficients for CO2

Dear all, I am using rigid CO2 model with virtual sites. The bond lengthe and LJ parameters are taken from TraPPE force field (Vapor–liquid equilibria of mixtures containing alkanes, carbon dioxide, and nitrogen. JJ Potoff, JI Siepmann. AIChE journal 47 (7), 1676-1682, 2001. 469). I followe

Re: [gmx-users] Pi stacking

Hi Soumadwip, Did you see any difference at different salt concentrations? I doubt whether GROMACS can consider salt concentration. Just adding NA and CL doesn't produce the effect of salt concentration in GROMACS. If anybody think I am wrong and effect of salt concentration can be simulated using

Re: [gmx-users] How to add a repulsive harmonic potential

>This isn't mathematically consistent, nor do I think it will be stable. That >is >a massive repulsion at just about any distance. For a bit gentler approach, >please consider what we do with hydrophobic fragments here: >http://pubs.acs.org/doi/abs/10.1021/ci100462t Thank you for your advice

[gmx-users] how to make average hbond plot in gromacs using xmgrace

Dear all, i am trying to reduce the variation in the h-bond plot in xmgrace. can we reduce it and how? any help will be very appreciated with best regards -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Na

Re: [gmx-users] Pi stacking

As far as I know, AMBER force-fields tend to overestimate the stacking interactions in nucleic acids, whereas CHARMM tends to understabilize them. The Chen and Garcia paper talks extensively about it (HIgh-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulati

Re: [gmx-users] there wasn't md_0_1.xtc file

The errors mentioned in comment #2 indicates that the system is blowing up and it is not equilibrated well. It is writing separate step.PDB files since there are bad contacts. Probably your system is not properly equilibrated. By the way , i didnot understand what do you mean by 'running a covalen