Re: [gmx-users] Custom urea topology

I attached them but I think they didn't pass through. I put the three files (topol.top, eq.mdp, urea.gro) on this gist: https://gist.github.com/gabrielelanaro/8817709 On Tue, Feb 4, 2014 at 6:53 PM, Justin Lemkul wrote: > > > On 2/4/14, 9:17 PM, Gabriele Lanaro wrote: > >> Hi! I'm trying to w

[gmx-users] Regarding Free energy perturbation

When we convert some atoms to a dummy atom (DUM) in a B state topology, then does the Gromacs free energy code automatically take care of this transformation in bonded terms (bond, angle, dihedral etc.) because we can not define B state parameters corresponding to bonded terms of dummy atoms in a t

Re: [gmx-users] OPLS force field issue....

On 2/4/14, 9:43 PM, Sidath Wijesinghe wrote: yes it worked. i only added CA CA CZ CZ 0.000 0.000 0.000 0.000 in diheadral block. since all 12 errors point the same kind of diheadral type. How did you decide these parameters were appropriate? You're essentially saying that the rotational b

Re: [gmx-users] Custom urea topology

On 2/4/14, 9:17 PM, Gabriele Lanaro wrote: Hi! I'm trying to write a custom topology for the urea molecule. Taken from the following paper http://pubs.acs.org/doi/abs/10.1021/jp030534x. I generated the bonds, angles, torsional dihedrals and improper dihedrals. The scenario is as follows: 1) I

Re: [gmx-users] OPLS force field issue....

yes it worked. i only added CA CA CZ CZ 0.000 0.000 0.000 0.000 in diheadral block. since all 12 errors point the same kind of diheadral type. Then i tried to mdrun...i got this error message Fatal error: 1 particles communicated to PME node 6 are more than 2/3 times the cut-off out of the d

[gmx-users] Custom urea topology

Hi! I'm trying to write a custom topology for the urea molecule. Taken from the following paper http://pubs.acs.org/doi/abs/10.1021/jp030534x. I generated the bonds, angles, torsional dihedrals and improper dihedrals. The scenario is as follows: 1) If I leave the bonds section the thing works wit

Re: [gmx-users] gdist: command not found

On 2/4/14, 6:16 PM, Chetan Mahajan wrote: Hi, I am trying to run gdist command on supercomputing system Stampede. Even though I enter full path to Gromacs installed, it gives error--gdist: command not found. Could you tell me the real issue here? export PATH=/opt/apps/intel13/mvapich2_1_9/gro

[gmx-users] gdist: command not found

Hi, I am trying to run gdist command on supercomputing system Stampede. Even though I enter full path to Gromacs installed, it gives error--gdist: command not found. Could you tell me the real issue here? export PATH=/opt/apps/intel13/mvapich2_1_9/gromacs/4.6.3/bin:$PATH gdist -f lnanop.xtc -s l

Re: [gmx-users] Old charmm force field

On 2/4/14, 5:46 PM, Mark Abraham wrote: IIRC 19 had only protein and same as 27! CHARMM19 did indeed have only protein parameters, but CHARMM27 isn't actually a protein force field, it's nucleic acids :) CHARMM19 is united-atom, while all of the more recent versions of the force field (CH

Re: [gmx-users] Replica Exchange Molecular Dynamics

Hi, I have posted this query two times in the forum, but got no reply. Can anybody give an advice on the following question ... I am trying to apply the REMD to study the difference between the folding free energy of a 24 residue peptide with two different conformations. As I am short of requir

Re: [gmx-users] Old charmm force field

IIRC 19 had only protein and same as 27! Mark On Feb 4, 2014 8:55 PM, "Sanku M" wrote: > Hi > I need to reproduce a simulation result which had been performed using a > very old version of charmm forcefield (PARAMh19 forcefield). In order to > reproduce it correctly, I would like to use same f

[gmx-users] Rigid nanotube

Dear Gmx Users, I have 5 types of atoms which create a shape of the nonotube. 5 types of beads correspond to future appliaction to which I will attach protein. I wish the nanotube to be rigid and move in XY directions only. I created bonds between all of them with app. b0=0.34 nm and a force const

[gmx-users] Old charmm force field

Hi   I need to reproduce a simulation result which had been performed using a very old version of charmm forcefield (PARAMh19 forcefield). In order to reproduce it correctly, I would like to use same forcefield that had been used there. I wonder whether there is any gromacs version of this old ch

Re: [gmx-users] [gmx-developers] bonding problem in simulating multiple objects in the same box

This is not an appropriate question for the development list; please post to gmx-users. You got a reply to this same question already: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-February/087017.html If there are further questions based on that response, please post tho

Re: [gmx-users] DNA with charmm27 works fine but why

On 2/4/14, 12:52 PM, gromacs query wrote: When running grompp, yes, the order is significant and the coordinates must match the topology. am little confused about 'coordinates'. Say if I have two structures which are well equlibrated and just represent two different configurations and also th

Re: [gmx-users] DNA with charmm27 works fine but why

>> When running grompp, yes, the order is significant and the coordinates must match the topology. am little confused about 'coordinates'. Say if I have two structures which are well equlibrated and just represent two different configurations and also the atom order matches with some common top fi

[gmx-users] bonding problem in simulating multiple objects in the same box

hi, i am new to gromacs. i was trying simulate multiple (eg. 3 or 4 ) carbon nanotubes in a single box. The way I am trying to do is ... 1. Take both pdb files, merge them(using pymol) according to my orientation and create a single pdb file for the whole structure. 2. Generate the gro and hence t

Re: [gmx-users] DNA with charmm27 works fine but why

On 2/4/14, 12:35 PM, gromacs query wrote: Hi Justin Presence of the correct atoms is the only absolute requirement Thanks. Correct 'atoms' mean correct 'atom names'? so does that mean I should rename my atoms according to rtp file? Yes, atom names need to match. That's all that's in a c

Re: [gmx-users] DNA with charmm27 works fine but why

Hi Justin >> Presence of the correct atoms is the only absolute requirement Thanks. Correct 'atoms' mean correct 'atom names'? so does that mean I should rename my atoms according to rtp file? Also one more question: I think atom order does matter when I load a pdb and use some .top file? (and i

Re: [gmx-users] wall problem

On 02/04/2014 06:02 PM, Justin Lemkul wrote: That shouldn't happen if the compressibility is zero. I can't suggest anything else; the "incompressible along z" approach should work, but I have no experience with it. As stated in the other thread, there is a large burden of proof when doing tri

Re: [gmx-users] DNA with charmm27 works fine but why

On 2/4/14, 11:50 AM, gromacs query wrote: Hi All I have built DNA with NAB in AMBER and it provide names as D*, D*3, D*5 (where * = A,T,G,C) and want to use charmm27 in gromacs. The charmm27.ff/dna.rtp does not have D*5 or D*3 and has only D* residues, so I renamed D*5 or D*3 to just correspon

Re: [gmx-users] wall problem

On 2/4/14, 11:13 AM, Albert wrote: On 02/04/2014 05:01 PM, Justin Lemkul wrote: This is exactly the same issue that was discussed last week. Please read those posts. -Justin I found that and have the following settings: compressibility = 4.5e-5 0 but I don't know why the problem is st

[gmx-users] DNA with charmm27 works fine but why

Hi All I have built DNA with NAB in AMBER and it provide names as D*, D*3, D*5 (where * = A,T,G,C) and want to use charmm27 in gromacs. The charmm27.ff/dna.rtp does not have D*5 or D*3 and has only D* residues, so I renamed D*5 or D*3 to just corresponding D* residues. The output pdb with pdb2gmx

Re: [gmx-users] wall problem

On 02/04/2014 05:01 PM, Justin Lemkul wrote: This is exactly the same issue that was discussed last week. Please read those posts. -Justin I found that and have the following settings: compressibility = 4.5e-5 0 but I don't know why the problem is stil there: the vacuum layer disappe

Re: [gmx-users] wall problem

On 2/4/14, 10:59 AM, Albert wrote: Hello Justin: I took your advices and submit the system to MD simulations. After NVT, the vacuum layer was still there. However, my pbc box shrinked to its orginal size after NPT, and the vacuum layer was disapeared here is my compreasiblity settings: ;

Re: [gmx-users] wall problem

Hello Justin: I took your advices and submit the system to MD simulations. After NVT, the vacuum layer was still there. However, my pbc box shrinked to its orginal size after NPT, and the vacuum layer was disapeared here is my compreasiblity settings: ; Pressure coupling parameters pcou

Re: [gmx-users] multiple GPU on multiple nodes

John, I strongly suggest that you consult the Blue Waters or other XK7 manual or talk to the support team. Understanding this hardware in crucial in getting any reasonable performance. As I said before, the inconsistency in your commands is that you request nnodes x nppn = 2 x 16 MPI ranks which

Re: [gmx-users] multiple GPU on multiple nodes

On Tue, Feb 4, 2014 at 1:51 AM, cyberjhon wrote: > Dear Szilárd > > Thanks for your answer. > > To submit the job I do; > > qsub -l nodes=2:ppn=16,walltime=12:00:00 > > Then, to run gromacs I can do: > aprun -n 1 mdrun_mpi -deffnm protein >Those qsub and aprun commands are not in lik

[gmx-users] TUBE - Lincs or bonds?

Dear Gmx Users, I have a tube made of atoms connected in lines: Picture here: http://speedy.sh/BTRHx/tube.png The edges of the tube are on the box edges with pbc - tube is infinite in lenght then. I wish this tube to move only in XY directions so I froze the Z coordinate using freezedim and free

Re: [gmx-users] wall problem

On 02/04/2014 02:50 PM, Justin Lemkul wrote: Elongate the box in the z-dimension and set its compressibility to zero in the .mdp file. This issue was discussed at length just a few days ago. Beware possible ordering artifacts of the interfaces. -Justin Hi Justin: many thanks for your fur

Re: [gmx-users] question about gromacs

Hi, As genrestr -h warns, you need a position restraint files per moleculetype, not for the whole set of such molecules. Mark On Tue, Feb 4, 2014 at 2:39 PM, Andrew Bostick wrote: > Hi all > > My system contain dopc + cholesterol + water + drug molecules. > > I want to do MD simulation with po

Re: [gmx-users] question about gromacs

On 2/4/14, 8:43 AM, Andrew Bostick wrote: I used following line in mdp file: define = -DPOSRES_dopc -DPOSRES_chol Is my manner true? To do what? That will trigger the #include statements in the topology, but the error message shown below indicates that you have not correctly created

Re: [gmx-users] wall problem

On 2/4/14, 2:58 AM, Albert wrote: Thanks a lot for such helpful suggestions. I am struggled to the question how to add a vacuum layer to the system. Unfortunately I didn't find any tutorial or detailed thread on this topic. Does any body have any suggestions? Elongate the box in the z-dimen

Re: [gmx-users] AMBER99sb-ILDN - protonated C-terminus

On 2/4/14, 5:15 AM, Marieke Schor wrote: Hi, I would like to test the effect of low pH on the stability of my protein hexamer. For the neutral pH case I used the AMBER99sb-ILDN forcefield but this appears not to have parameters to describe a protonated C-terminus. I can only find one paper that

Re: [gmx-users] Spacing between Umbrella sampling

On 2/3/14, 10:14 PM, Arunima Shilpi wrote: Hello sir Many many thanks for your suggestion. Here I generated the distances files using your tutorial for Umbrellla sampling (perl distances.pl). The confiugration I have selected was done manually . These co-ordinates mentioned with spacing of 0.

Re: [gmx-users] OPLS force field issue....

On 2/3/14, 10:14 PM, Sidath Wijesinghe wrote: Justin,, i rechecked the opls/ff that i used and found some errors, after correction them i got the .top file. note that i was able to define the charge groups as well. when i use this .top file with grompp, now am getting 12 errors...as follwos..

[gmx-users] DNA simulation with opls forcefield

Dear all, I want to do a all-atom simulation of protein-DNA complex using gromacs with opls forcefield. I see that the nucleic acid files are available at this site ( http://rnp-group.genebee.msu.su/3d/ff.htm ) Can anyone let me know how to incorporate these files and run the simulation ? Also, A

Re: [gmx-users] question about gromacs

I used following line in mdp file: define = -DPOSRES_dopc -DPOSRES_chol Is my manner true? On Tue, Feb 4, 2014 at 5:09 PM, Andrew Bostick wrote: > Hi all > > My system contain dopc + cholesterol + water + drug molecules. > > I want to do MD simulation with position restraint on dopc and c

[gmx-users] question about gromacs

Hi all My system contain dopc + cholesterol + water + drug molecules. I want to do MD simulation with position restraint on dopc and cholesterol molecules. I used following lines to obtain posre*.itp files: genrestr -f npt.gro -n index.ndx -o posre_dopc.itp genrestr -f npt.gro -n index.ndx -o

Re: [gmx-users] multiple GPU on multiple nodes

OK, thanks! :-) Mark On Tue, Feb 4, 2014 at 12:20 PM, Szilárd Páll wrote: > On Tue, Feb 4, 2014 at 2:31 AM, Mark Abraham > wrote: > > On Tue, Feb 4, 2014 at 1:51 AM, cyberjhon wrote: > > > >> Dear Szilárd > >> > >> Thanks for your answer. > >> > >> To submit the job I do; > >> > >> qsub -l no

Re: [gmx-users] Molecular volume from trajectory

Thanks, sure I'll try it 2014-02-04 ABEL Stephane 175950 : > hello, > > In our group, we have developed a tool called "trjVoronoi" that computes > the molecular volume (i.e. Voronoi Volume) and the associated surfaces) of > the whole cell and each molecular components from MD trajectories genera

Re: [gmx-users] multiple GPU on multiple nodes

On Tue, Feb 4, 2014 at 2:31 AM, Mark Abraham wrote: > On Tue, Feb 4, 2014 at 1:51 AM, cyberjhon wrote: > >> Dear Szilárd >> >> Thanks for your answer. >> >> To submit the job I do; >> >> qsub -l nodes=2:ppn=16,walltime=12:00:00 >> >> Then, to run gromacs I can do: >> aprun -n 1 mdrun_mpi -deffnm

Re: [gmx-users] Molecular volume from trajectory

Hi, g_sas may be what you are looking for. Regards, On Tue, Feb 4, 2014 at 4:22 PM, Андрей Гончар wrote: > Hi all > Is there a tool to calculate molecular volume for a whole MD trajectory? > I.e. I'd like to see how does the molecule changes its volume during MD. > I know that there are many e

Re: [gmx-users] Molecular volume from trajectory

Hi, g_sas is the tool for you. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 4 Feb 2014, at 10:52, Андрей Гончар wrote: > Hi all > Is there a t

Re: [gmx-users] Molecular volume from trajectory

hello, In our group, we have developed a tool called "trjVoronoi" that computes the molecular volume (i.e. Voronoi Volume) and the associated surfaces) of the whole cell and each molecular components from MD trajectories generated with GROMACS or NAMD. You can download it here: https://sites

Re: [gmx-users] multiple GPU on multiple nodes

On Tue, Feb 4, 2014 at 1:51 AM, cyberjhon wrote: > Dear Szilárd > > Thanks for your answer. > > To submit the job I do; > > qsub -l nodes=2:ppn=16,walltime=12:00:00 > > Then, to run gromacs I can do: > aprun -n 1 mdrun_mpi -deffnm protein Those qsub and aprun commands are not in like with each ot

[gmx-users] Molecular volume from trajectory

Hi all Is there a tool to calculate molecular volume for a whole MD trajectory? I.e. I'd like to see how does the molecule changes its volume during MD. I know that there are many external tools for this purpose, but maybe I'm wrong and GROMACS already has something for that? Thanks in advance --

[gmx-users] AMBER99sb-ILDN - protonated C-terminus

Hi, I would like to test the effect of low pH on the stability of my protein hexamer. For the neutral pH case I used the AMBER99sb-ILDN forcefield but this appears not to have parameters to describe a protonated C-terminus. I can only find one paper that uses AMBER99sb-ILDN with protonated

Re: [gmx-users] Use g_wham on 2D PMF

g_wham does only 1D PMF but can handle several restrains. There is 2D code on Alan Grossfield website. Plumed refers to it. On Feb 3, 2014, at 5:54 PM, "DAI, JIAN" wrote: > Dear all: > Is it possible for g_wham to calculate 2D PMF? > It seems to me that g_wham can deal with this because the

Re: [gmx-users] wall problem

Thanks a lot for such helpful suggestions. I am struggled to the question how to add a vacuum layer to the system. Unfortunately I didn't find any tutorial or detailed thread on this topic. Does any body have any suggestions? thank you very much. Albert On 01/31/2014 06:10 PM, Thomas Piggot