Re: [gmx-users] Error with MARTINI depending by the box size

Tanks to all for your advices, I am going to check all the different aspect you suggested and I will report the results as soon as possible. Francesco 2012/12/11 Tsjerk Wassenaar > Hi, > > Visualization is the key. If you check the structure right after genbox, > you should be able to notice s

Re: [gmx-users] Error with MARTINI depending by the box size

I have not followed the thread but concerning the solvation of a protein using genbox you need to: 1- use a box of water that has the exact size of the final box you want (you make it yourself using any tool you want) and you need to define the box size of the protein file as the one of the

[gmx-users] Analysis of solvent dynamics

Dear Gromacs Users! I want to study dynamics of solvent burried into the protein interiour during simulation (to check solvent accessible area of different amino acid of my protein). Eg while simulating of Green Fluorescent protein I'd like to check how much water burried into the beta-can inter

[gmx-users] DNA simulation

Dear Gromacs users I want to simulate dobule strand DNA using gromacs. I have read that I should use amber forcefield for DNA simulation and I have crossed a web page explaining some parameters which I should change in gromacs package to become compatible with this amber force filed. 1) I wa

[gmx-users] Re: Pulling ion - US

I would also use the same residue from the pulling for the US. One thing you should be aware of is the pulling dimension: Now you have the pull-code only ativated for the z-direction. If you use this still in the US the ion can move freely in the xy-plane (freely in the sense of what is possible

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Peter, thanks for explanations! Could you tell me is it possible to convert CGenFF output for hetatomic group to the RTP (not an itp ) gromac's data ? I want to simulate in Gromacs ( in charmm 27 ff) qm\mm GFP protein which is consist of HETTATOMIC chromophore covently bonded to the polypeptid

Re: [gmx-users] Re: Pulling ion - US

I have made SMD simulations in order to separate a Ca2+ ion from its complexation site in the protein, which had charge of about -6 e. Without position constraints in the protein alpha carbons it unfolded in every pull simulation. 2012/12/11 Thomas Schlesier > wont happen, since the prob

Re: [gmx-users] Is there any tool in gromacs for calculating intermolecular interactions and intramolecular interactions indepedently?

Section 7.4 and chapter 8 of the manual discuss what functionality exists in the utility tools. If that doesn't help you need to be more specific about what you mean by "calculate interactions" Mark On Tue, Dec 11, 2012 at 2:15 PM, Wu Chaofu wrote: > Dear gmxers, > I am trying to calculate inte

Re: [gmx-users] gen-vel=no

On 12/11/12 1:19 AM, Venkat Reddy wrote: The check point file you submit will have the velocity information. A checkpoint file is indeed a better set of information to pass to -t, but it is not clear if the OP even used -t in the invocation of grompp. If not, there will be a discontinuity

Re: [gmx-users] Atom index (13154) in position_restraints out of bounds

On 12/11/12 1:23 AM, Yun Shi wrote: Hi all, I want to restrain the OW of a bound water molecule for the MD of a protein in water. But the index of this OW is apparently out of range and I know someone would suggest merging this water with my protein (e.g. put them in the same .itp file) so as

Re: [gmx-users] Atom index (13154) in position_restraints out of bounds

No. Bonded interactions (such as distance restraints) can only be defined between atoms present in the same [moleculetype]. OTOH a [moleculetype] doesn't care whether any bonded interactions exist between its atoms or not, so as long as you obey the constraint that the atom ordering implied by your

Re: [gmx-users] Is vacuum simulation NVT?

On 12/11/12 2:09 AM, Jong Wha Lee wrote: Dear Gromacs users, Is a vacuum md simulation an NVT simulaton? As the pressure and energy are not fixed, I think that the only option left is NVT. But without pbc, the volume would not have been defined. Can it still be called NVT? In the absence

Re: [gmx-users] Re: What is the purpose of the [ pairs ] section?

Hi Andrew! I've also been a bit confused by the names when I started looking at the force field definitions in GROMACS. Although Justin's replies contain all the information (as usual :)), let's try to shed some light with an example: consider a chain formed by atoms i-j-k-l-m-n; - means that ther

Re: [gmx-users] Umbrella sampling - chain A does not get pulled

On 12/11/12 2:40 AM, Davide Mercadante wrote: Dear Justin, I have been practicing umbrella sampling simulations following your tutorial step by step. I have just finished to perform the pull simulations to identify the configurations to use in the umbrella runs. I have used the distances.pl sc

Re: [gmx-users] DNA simulation

On 12/11/12 5:22 AM, delara aghaie wrote: Dear Gromacs users I want to simulate dobule strand DNA using gromacs. I have read that I should use amber forcefield for DNA simulation and I have crossed a web page explaining some parameters which I should change in gromacs package to become comp

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

On 12/11/12 6:04 AM, James Starlight wrote: Peter, thanks for explanations! Could you tell me is it possible to convert CGenFF output for hetatomic group to the RTP (not an itp ) gromac's data ? I want to simulate in Gromacs ( in charmm 27 ff) qm\mm GFP protein which is consist of HETTATOM

[gmx-users] Protein-POPC-water

 Dears, I am trying to simulate a system of water, POPC and protein using charmm36 ff. I follow the protocol suggested in KALP15-DPPC tutorial. I follow the tutorial step by step up to NVT equilibration without any bond or any  other type warnings. Then I run the grompp :   # grompp -f nvt.mdp

Re: [gmx-users] Protein-POPC-water

On 12/11/12 8:45 AM, Shima Arasteh wrote: Dears, I am trying to simulate a system of water, POPC and protein using charmm36 ff. I follow the protocol suggested in KALP15-DPPC tutorial. I follow the tutorial step by step up to NVT equilibration without any bond or any other type warnings.

[gmx-users] force autocorrelation

Hi Does anyone know if, and if so how, GROMACS can generate a force autocorrelation function? If this is not possible then can I extract the force exterted by each atom on a single labelled atom? Regards Ted -- View this message in context: http://gromacs.5086.n6.nabble.com/force-autocorrelati

Re: [gmx-users] GPU warnings

Hi Thomas, It looks like some gcc 4.7-s don't work with CUDA, although I've been using various Ubuntu/Linaro versions, most recently 4.7.2 and had no issues whatsoever. Some people seem to have bumped into the same problem (see http://goo.gl/1onBz or http://goo.gl/JEnuk) and the suggested fix is t

Re: [gmx-users] force autocorrelation

1. Run mdrun with nstfout set appropriately 2. g_traj -h 3. g_analyze -h 4. Profit! Mark On Tue, Dec 11, 2012 at 3:31 PM, khuws wrote: > Hi > Does anyone know if, and if so how, GROMACS can generate a force > autocorrelation function? > If this is not possible then can I extract the force exter

[gmx-users] Essential dynamics (ED) sampling using make_edi

Hello All, I want to use the essential dynamics (ED) sampling method to simulate the unfolding to folding process using make_edi option of GROMACS. For this task I am using -radcon option (acceptance radius contraction along the first two eigenvectors towards the folded structure (b4md.gro)) of m

Re: [gmx-users] glibc error

We don't yet have enough information to help you. What GROMACS version? Does it happen under other conditions? Mark On Tue, Dec 11, 2012 at 9:06 AM, vahid garshasbi wrote: > hi > when I run g_density in X AND Y direction in my program I have this error: > *** glibc detected *** g_density: munmap

Re: [gmx-users] GPU warnings

Am 11.12.2012 16:04, schrieb Szilárd Páll: It looks like some gcc 4.7-s don't work with CUDA, although I've been using various Ubuntu/Linaro versions, most recently 4.7.2 and had no issues whatsoever. Some people seem to have bumped into the same problem (see http://goo.gl/1onBz or http://goo.gl/

Re: [gmx-users] GPU warnings

On Tue, Dec 11, 2012 at 6:49 PM, Mirco Wahab < mirco.wa...@chemie.tu-freiberg.de> wrote: > Am 11.12.2012 16:04, schrieb Szilárd Páll: > > It looks like some gcc 4.7-s don't work with CUDA, although I've been >> using >> various Ubuntu/Linaro versions, most recently 4.7.2 and had no >> issues what

[gmx-users] intermolecular rdfs for a bulky cation

Hi, I need to calculate intermolecular rdfs b/w atoms of P+14,6,6,6 cations on gromacs. The cation has three, 6 carbon tails , a 14 carbon (long) tail and a P at the center. I used nrexcl=21 in the .top file. I believe this job needs a lot memory and the job dies after some time. 1) How ca

Re: [gmx-users] Is vacuum simulation NVT?

> In the absence of PBC, you simply have an infinite system. In a loose > sense, that may be NVT, but V is infinite, so whether or not you can > consider that to be constant or not is theoretical math above what I know :) A real molecule in vacuum is usually NVE -- it is not coupled to the enviro

[gmx-users] Re: force autocorrelation

Thanks, I forgot to mention that I need the force autocorrelation for the forces acting on a single atom. Will the method 1. Run mdrun with nstfout set appropriately 2. g_traj -h 3. g_analyze -h work here Keith -- View this message in context: http://gromacs.5086.n6.nabble.com/force-autoc

Re: [gmx-users] Re: force autocorrelation

Yes. Read about analysis groups in chapter 8. Mark On Tue, Dec 11, 2012 at 8:20 PM, khuws wrote: > Thanks, > I forgot to mention that I need the force autocorrelation for the forces > acting on a single atom. Will the method > > 1. Run mdrun with nstfout set appropriately > 2. g_traj -h > 3. g_

[gmx-users] Re: What is the purpose of the [ pairs ] section?

Hi Javier, Mark, Justin, and Bogdan, Thank you SO much for your time! The responses that you gave are INCREDIBLY helpful to me. I think that they will be very useful, too, to future users as helpful canonical answers. If you have time, I have another question related to the [ pairs ] section.

Re: [gmx-users] Re: What is the purpose of the [ pairs ] section?

On 12/11/12 3:36 PM, Andrew DeYoung wrote: Hi Javier, Mark, Justin, and Bogdan, Thank you SO much for your time! The responses that you gave are INCREDIBLY helpful to me. I think that they will be very useful, too, to future users as helpful canonical answers. If you have time, I have anoth

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Today I've made parametrization of the chromophore group by means of Swiss param and integrated that topology into charmm27 ff. The only problem that I have is with the N-term N atom of the chromophore. It's likely that I made mistake to parametrize it into full protonated form (NH2). When I've us

Fw: [gmx-users] intermolecular rdfs for a bulky cation

> Hi, > > I need to calculate intermolecular rdfs b/w > P+14,6,6,6 cations. The cation has three, 6 > carbon tails ,  a 14 carbon (long) tail and a Phosphorous at the > center. > > I used nrexcl=21 in the .top file. > > I believe this job needs a lot of memory and the job dies after > some

[gmx-users] Solvating Podophyllotoxin in ethanol

Dear Gromacs users, I've been trying to solvate  Podophyllotoxin in ethanol. I used chimera and acpype to create PPT and I got the .itp and .pdb files. For ethanol I used http://virtualchemistry.org/molecules/64-17-5/index.php .top and GAFF liquid structure .pdb file. Since some atomtypes match b

[gmx-users] g_x2top help

Hi Gromacs users I have a problem Im trying to form a .top file using a g_x2top -f -o -ff command. I have defined .n2t .rtp .itp files. and wanted to construct a topology file. but the script does not identify any of the atoms from .gro file. my .n2t file ; clayff ; n2t H    h*    0.4100   

[gmx-users] apply force to the protein

Dear all I want to apply a force to only one direction of the protein to let it go through a pore, can gromacs meet my needs? thank you. -- Regards Congyue Wang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at h

Re: [gmx-users] apply force to the protein

On 12/11/12 4:55 PM, Congyue Wang wrote: Dear all I want to apply a force to only one direction of the protein to let it go through a pore, can gromacs meet my needs? Yes. Read about the pull code in the manual. -Justin -- Justin A. Lemkul, Ph.D. R

Re: [gmx-users] g_x2top help

On 12/11/12 4:40 PM, Milinda Samaraweera wrote: Hi Gromacs users I have a problem Im trying to form a .top file using a g_x2top -f -o -ff command. I have defined .n2t .rtp .itp files. and wanted to construct a topology file. but the script does not identify any of the atoms from .gro file.

Re: [gmx-users] Solvating Podophyllotoxin in ethanol

On 12/11/12 4:30 PM, Hovakim Grabski wrote: Dear Gromacs users, I've been trying to solvate Podophyllotoxin in ethanol. I used chimera and acpype to create PPT and I got the .itp and .pdb files. For ethanol I used http://virtualchemistry.org/molecules/64-17-5/index.php .top and GAFF liquid s

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

On 12/11/12 4:13 PM, James Starlight wrote: Today I've made parametrization of the chromophore group by means of Swiss param and integrated that topology into charmm27 ff. The only problem that I have is with the N-term N atom of the chromophore. It's likely that I made mistake to parametrize i

[gmx-users] pbs not returning gromacs files

I'm not sure if this is the right place to be asking this but I haven't been able to find an answer. I'm using a pbs script to submit a parallel job of the water tutorial. So in my home file I have all of the files from the water tutorial and the output from grompp. If I submit my simulation

Re: [gmx-users] g_x2top help

Please keep the discussion on the gmx-users mailing list. On 12/11/12 5:12 PM, Milinda Samaraweera wrote: Hi Justin error is Could only find a forcefield type for 0 out of 2808 atoms I attached my input files, and I checked .gro for errors. cant find any I don't exactly know what you've c

Re: [gmx-users] pbs not returning gromacs files

On 12/11/12 5:10 PM, John Doe wrote: I'm not sure if this is the right place to be asking this but I haven't been able to find an answer. I'm using a pbs script to submit a parallel job of the water tutorial. So in my home file I have all of the files from the water tutorial and the output

[gmx-users] g_densmap: adsorbed species and output format

Dear Gromacs users, I am writing to ask about g_densmap command: If there are species adsorbed (stagnant) or structured around a frozen group, for which I want to obtain the density distribution map, g_densmap calculates unrealistically high densities. (like 2000 /nm3 of water...). So in visuali

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

That the mollecule that I made [ CRO ] [ atoms ] CG2 CB 0.0284 0 CD1 CB -0.1500 1 CD2 CB -0.1500 2 CE1 CB -0.1500 3 CE2 CB -0.1500 4 CZCB 0.0825 5 HLH 0.3600 39 NRNH1-0.9900 6 CA1 CR 0.3310 7 CB1 CR 0.2800 8 CG1 CR 0.

[gmx-users] Re: Re: Is vacuum simulation NVT?

Thank you very much Justin, and thank you very much Michael. Your replies were of a great help. Jong Wha -- 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/Searc

[gmx-users] Poteintial energy of my system

Dear users, I ran grompp on my system: #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr #mdrun -deffnm em When I get the ouput, the potential energy is a positive integer, I think it doesn't seem sensible. Does it? Steepest Descents converged to Fmax < 100 in 4998 steps Po