[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

2015-03-22 Thread Alex
on aromatics, which can and should be further refined. All input is greatly appreciated and I'd especially love to hear from the Gromacs superhero Justin Lemkul. :) Thanks! Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

2015-03-24 Thread Alex
You guys have thought of everything, haven't you... :) Thanks. JL On 3/23/15 9:09 PM, Alex wrote: Great, thanks. One other question, just sort of jumping way ahead. Let's say I had a denaturated protein chain I wanted to drag in a simulation of translocation. Is there anything in Gromacs

[gmx-users] OPLS/AA support for DNA

2015-03-25 Thread Alex
understanding). There are some reasons I'd like to stick with oplsaa with my project. Not set in stone, but highly desirable. Any ideas? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

Re: [gmx-users] Setting custom atoms in FF

2015-03-30 Thread Alex
syntax to do that? I just want to define my atoms in a way that supplements (actually, precedes) what x2top does when the atoms are not specifically labeled. A tedious solution in my case, but definitely viable, if this works. Thank you, Alex JL On 3/29/15 7:53 PM, Alex wrote: Another

Re: [gmx-users] Density of pure tetrolic acid does not agree with experimental data

2015-03-31 Thread Alex
interactions. Alex NKH Hello Gromacs users, NKH I tried to create a 6.5 nm cubic box of tetrolic acid (otherwise NKH known as 2-butynoic acid), but the density is too low. According NKH to this, http://www.chemspider.com/Chemical-Structure.61810.html, NKH the density should be about 0.964 NKH g/mL

Re: [gmx-users] Setting custom atoms in FF

2015-03-31 Thread Alex
know x2top has limited intelligence, but how is this correct program behavior? Also, is there any way to tell x2top to copy all bond and angle parameters from the ff data into the topology the way pdb2gmx does? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Setting custom atoms in FF

2015-03-31 Thread Alex
Building things is not necessary. I just wasn't sure what particular field in PDB you were talking about. Some indication that it is supposed to work is enough. ;) Thanks, Alex JL I don't have the time or desire to build something, test it, and give you an JL absolute answer :) I can only

Re: [gmx-users] Setting custom atoms in FF

2015-03-29 Thread Alex
be extremely useful. One could always use the default value if no setting is entered. Could the last point be relayed to the developers? Sounds like a huge necessity to me, to be honest. Thank you, Alex JL On 3/29/15 4:07 PM, Alex wrote: Hi all, I am messing with the OPLS/AA forcefield. The idea

[gmx-users] Setting custom atoms in FF

2015-03-29 Thread Alex
a globally neutral system. Here is the problem: x2top ignores the second statement from above and the functionalized edge C is assigned #996. Aside from manually modifying the resulting topology, can we make this distinction stick? Thanks, Alex -- Gromacs Users mailing list * Please search

Re: [gmx-users] Setting custom atoms in FF

2015-03-29 Thread Alex
Yeah, I know there's that disclaimer. I wonder if this http://software-lisc.fbk.eu/obgmx/ could be useful. Any comment on this UFF? First time I'm hearing about it, to be honest. The system I have in mind isn't much beyond CNTs and nucleotide chains. Well, and water. Thanks. Alex JL g_x2top

Re: [gmx-users] Setting custom atoms in FF

2015-03-29 Thread Alex
just discovered that a bunch of different atoms isn't set up correctly. Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] OPLS/AA support for DNA

2015-03-26 Thread Alex
come from solid-state systems and wish I had experience with Gromacs that's beyond editconf-genbox-pdb2gmx-grompp. Come to think of it, you'd set up my system in about an hour. Care to collaborate? :))) Alex JL On 3/26/15 6:10 PM, Alex wrote: Yeah, I agree with Justin, this is pretty half-baked

Re: [gmx-users] OPLS/AA support for DNA

2015-03-26 Thread Alex
oplsaa. Alex On Thu, Mar 26, 2015 at 3:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/26/15 8:30 AM, Smith, Micholas D. wrote: There was some work on OPLS-AA/L on nucleic acids back in version 3 of GROMACS. The group that did the work has a website where they discuss the nucleic

Re: [gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

2015-03-23 Thread Alex
will try the earlier suggestion and add the bonded definitions on top of what was suggested. Alex JL For this, the cleanest approach is to create a custom force field, and its JL contents should be rather simple - bonded and nonbonded parameters for some C JL type (for the CNT) and whatever

Re: [gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

2015-03-23 Thread Alex
ve in mind is one of those, as I'm sure many other researchers have. It just happens to involve graphene. ;) So, it may be worthwhile to gain some level of flexibility to define our own bonded parameters, if covalent bond creation/breake is not on the table. Thanks, Alex I was in your

Re: [gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

2015-03-23 Thread Alex
, and the sheet behaves beautifully and respects my PBC (the box has precise in-plane dimensions). I have solvated my sheet with quite a bit of SPC water (~32K molecules), about to test some energy minimization followed by a dynamic simulation. Does the above sound reasonable? Thanks, Alex p.s

Re: [gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

2015-03-23 Thread Alex
Great, thanks. One other question, just sort of jumping way ahead. Let's say I had a denaturated protein chain I wanted to drag in a simulation of translocation. Is there anything in Gromacs for that, aside from fake charges and external electric fields, or messing with the code itself? JL Yep.

[gmx-users] The largest charge group contains [GIANT CRAPTON] of atoms

2015-04-01 Thread Alex
, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

[gmx-users] GMX-compatible DNA coordinates

2015-04-02 Thread Alex
of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy. I will really appreciate any suggestions. Thank you, Alex -- Gromacs Users mailing list * Please search

Re: [gmx-users] GMX-compatible DNA coordinates

2015-04-03 Thread Alex
Mauricio, That is very useful, thanks a lot. I'll try it in a bit. Alex MEN Alex, MEN You can use X3DNA to produce any nucleic acid geometry you’d like and MEN gromacs pdb2gmx will understand it. MEN For example, to create a single-strand of 16 DNA bases you only need a file MEN

Re: [gmx-users] GMX-compatible DNA coordinates

2015-04-03 Thread Alex
shouldn't hinder research. I do think that having a person such as yourself of Justin on my team to implement what I have in mind would speed things up tremendously, but noone seems to be interested, hint-hint. ;) Thanks, Alex Hi Alex, Writing a sed oneliner is not the same as writing

Re: [gmx-users] GMX-compatible DNA coordinates

2015-04-03 Thread Alex
ignored. Obviously, I welcome anything you can suggest. If this boils down to me writing a renaming script, so be it. :) Thanks, Alex On 03/04/2015 5:53 pm, "Mark Abraham" mark.j.abra...@gmail.com wrote: Hi, I tried that search myself and found some things that looked p

Re: [gmx-users] CNT force field and simulation

2015-04-11 Thread Alex
Great, glad it's working. I think there was a wrong bond length somewhere in Andrea's tutorial, not sure where exactly (I could be wrong). Look at everything carefully and make sure the bond lengths are at 0.142 nm, because this is what the generator is doing. Have fun! Alex ​Thank

Re: [gmx-users] CNT force field and simulation

2015-04-11 Thread Alex
'constraints = none' in your mdp. Constraint algorithms generally beloved by the biophysical community will turn your nanotubes into solid bricks. Good luck! Alex PB Hi everyone, PB I am new in the Gromacs users community and in the MD field too. However I PB red a lot and I want to realize simulation

Re: [gmx-users] hydrocarbons simulation

2015-04-11 Thread Alex
Like, a bond between father and son, fixing an old truck together. Sorry, sorry, I just couldn't pass by. :) JL What exactly would constitute a special bond in an alkane? JL -Justin -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] CNT force field and simulation

2015-04-11 Thread Alex
Hey Pierre, What exactly are you using to generate your structures? Strip the CONECT statements, they will be ignored, and it is not anything to worry about. Alex Hello Alex, Thank you a lot for your answer and I will do this tutorial again and again. I have tried some generators

Re: [gmx-users] CNT force field and simulation

2015-04-13 Thread Alex
-- and that is all you need to run a simulation. Alex On Mon, Apr 13, 2015 at 5:49 PM, Pierre Bertin bertin...@gmail.com wrote: Hi Alex, All right, I red all this weekend and I know how to modify a force field to add residues (I hope... ahah). I modified OPLSAA force field because I want

Re: [gmx-users] CNT force field and simulation

2015-04-13 Thread Alex
that is broadly inappropriate for solid-state systems. So, understanding the concept of topology in GMX-like packages is extremely useful. Gromacs has a manual of outstanding quality, and it should become your Holy Bible. :) Alex On Mon, Apr 13, 2015 at 6:31 PM, Alex nedoma...@gmail.com wrote: Hi

Re: [gmx-users] Maximum Force constant for Position Restraints

2015-04-21 Thread Alex
to be really hardcore about it, and still assume there _is_ such a thing as harmonic restraints, then the timestep of the real world is your Planck's time. :) Alex On Tue, Apr 21, 2015 at 1:36 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Thanks Alex. But then, theoretically

Re: [gmx-users] Maximum Force constant for Position Restraints

2015-04-21 Thread Alex
of the Nyquist theorem. I believe GMX tests for high vibrational frequencies according to 20*pi*tau on the left (ten times the period). Hope this helps. Alex On Tue, Apr 21, 2015 at 1:02 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hi guys! Is there a maximum value of Force Constant

Re: [gmx-users] Maximum Force constant for Position Restraints

2015-04-21 Thread Alex
Correction: tau/pi on the left for the highest value and 5*tau/pi for the 10 x period suggestion above. On Tue, Apr 21, 2015 at 1:13 PM, Alex nedoma...@gmail.com wrote: I think this can be estimated from a general physical argument. The absolute max in my opinion should come from 4*pi*tau

Re: [gmx-users] help on Graphene Nano Sheets

2015-04-23 Thread Alex
, but this is the paradigm. Good luck! Alex MC I run a graphene nanolayer, usin the below description (from previous mail. MC Now i got an other error. It look like there is a conflict in a force MC field system, someone can suggest me how to modify it? MC the force field file came from Minoia

Re: [gmx-users] pdb2gmx and protonated states of the residues

2015-04-25 Thread Alex
, nothing chanes. Alex B Dear All, B B By H++ and reduce we can have the input PDB for pdb2gmx have the B initial corrected protonated states for some residues, for example, B HIS, ARG, GLU and terminal residues. However biologically speaking with the change of the protein B conformation

Re: [gmx-users] pdb2gmx and periodic molecule

2015-04-25 Thread Alex
that. :) Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman

Re: [gmx-users] pdb2gmx and periodic molecule

2015-04-26 Thread Alex
Well, none of us in this project have the scripting skills necessary for this, that's sort of the problem... Thanks, Alex Hi Alex, I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA ACGT You would generate TACGTA

Re: [gmx-users] pdb2gmx and periodic molecule

2015-04-25 Thread Alex
. Is it that the utility behavior cannot be changed at the ff level, and thus our only option is manual modification of the topology? Thank you, Alex JL pdb2gmx isn't designed to intuitively handle such cases. The best way to go JL about it is: JL 1. Run pdb2gmx normally to add H that you might

Re: [gmx-users] Maximum Force constant for Position Restraints

2015-04-22 Thread Alex
the particle. Actually, come to think of it, my Planck time estimate for Mother Nature's timestep in vibrating bonds is probably incorrect. Effective bond length over the speed of light is more like it. :) Alex DvdS But it boils down to that if you make the force constant very large you DvdS need

Re: [gmx-users] help on Graphene Nano Sheets

2015-04-22 Thread Alex
correspond to what he's got. Alex MC Hi, MC i am trying to model a Graphene nano sheet GNS on Gromacs- MC I follow the advices about the nanotubes presented in the help site. MC _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ MC I run this command to greate the topology: MC

[gmx-users] pdb2gmx and periodic molecule

2015-04-24 Thread Alex
pbc, but we're not using it here. So, no topology in sight. Any ideas? Thanks, Alex p.s. I can post the test structure if there's any doubt about periodicity of the structure itself. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] help on Graphene Nano Sheets

2015-04-24 Thread Alex
to actually read the manual on the definition of angles and dihedrals. Energy minimization destroys the sheet, because there's a mess in your setup. Alex MC Hi people, MC I was able to run the graphene layer sheet, by follow your advices. MC I had a problem with the dihetral angle, MC i solved

Re: [gmx-users] pdb2gmx and periodic molecule

2015-04-25 Thread Alex
Yeah, I was trying to avoid that last part. You can tell by now how much I dislike uhm doing work. :) I'll try it, thanks. Alex JL 4. Manually edit the topology to introduce the needed bond, angles, and dihedrals. JL -Justin -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Pull code

2015-04-22 Thread Alex
Well, no, i don't want two. I want one! :) On Wed, Apr 22, 2015 at 5:17 PM, Ming Tang m21.t...@qut.edu.au wrote: Hi,Alex You can try constraint. In umbrella, both 2 groups move. Sent from my Huawei Mobile Alex nedoma...@gmail.com wrote: Hi all, I have a group (DNA) I'd like

Re: [gmx-users] Pull code

2015-04-22 Thread Alex
applied to the pulled group. So, if the periodic option is used, will it be possible to continuously translocate a linear chain with a length comparable to the corresponding box dimension, while the rest of the system is non-translating? Thanks as always. Alex On Wed, Apr 22, 2015 at 6:41 PM

Re: [gmx-users] Pull code

2015-04-22 Thread Alex
That is not an option for me, all groups must exhibit full dynamics, so partial restraint seems like a decent option. It is my understanding that explicitly moving only one group is impossible in the new version. Is that the case? Thanks, Alex On Wed, Apr 22, 2015 at 5:58 PM, Ming Tang m21.t

Re: [gmx-users] help on Graphene Nano Sheets

2015-04-22 Thread Alex
0.000 0.000 2GRA C2 -0.123 0.071 0.000 3GRA C3 -0.123 0.213 0.000 4GRA C4 0.000 0.284 0.000 5GRA C5 0.246 0.000 0.000 thanks Il 22/04/2015 19:46, Alex ha scritto: Hello, The forcefields for CNT and graphene

Re: [gmx-users] Pull code

2015-04-22 Thread Alex
The CNT group is actually very strongly restrained, not the entire atomic population, but the edges. So, from inspecting my code, everything looks right? Thanks, Alex Not really. The constraint option keeps a rigid constraint between the two groups. The umbrella keyword specifies

[gmx-users] Pull code

2015-04-22 Thread Alex
a single value. The simulated time is now about 1.5 ns. Thank you, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] help on Graphene Nano Sheets

2015-04-22 Thread Alex
You don't need to run x2top on the GRO file, you can apply it directly to the PDB. It seems like the PDB to GRO conversion destroyed the coordinates due to poor formatting of the initial coordinates. This has nothing to do with the forcefields or graphene, you may just have a crappy PDB. Alex

Re: [gmx-users] Problems in the modelling of interaction between peptide and copper

2015-04-23 Thread Alex
interaction and then try to use it to parameterize a lower level method such as MD. Hope this helps. Alex MT Dear all, MT I got a problem when modelling the interaction of a peptide and MT copper. I am using the force field of opls-aa. The charge of MT copper atoms are defined as zero and the non

Re: [gmx-users] Problems in the modelling of interaction between peptide and copper

2015-04-23 Thread Alex
Also, I assumed by copper you meant an actual surface of copper, not a few copper ions floating in water. :) Alex MT Dear all, MT I got a problem when modelling the interaction of a peptide and MT copper. I am using the force field of opls-aa. The charge of MT copper atoms are defined as zero

Re: [gmx-users] Constraints applied for keeping rigid in ND

2015-04-20 Thread Alex
just trying to see if these constraints are masking something really wrong with the unconstrained setup. You see, noone uses constraints in solid-state simulations, the structure must be conserved, unless something is seriously wrong. Alex On Apr 20, 2015 10:34 AM, hang yin yinhang...@gmail.com wrote

Re: [gmx-users] Constraints applied for keeping rigid in ND

2015-04-20 Thread Alex
, which once again could include the time step. Diamond structure, if properly set up, should be quite rigid, even if your bond/angle terms are somewhat off, because, well, it's the diamond structure. Alex hy Hi all, hy My research focuses on the dynamics of a nanodiamond(ND) in a biological hy

Re: [gmx-users] Constraints applied for keeping rigid in ND

2015-04-20 Thread Alex
Also, I just looked at your topology. Where are your angles? Try to implement them and then turn off constraints. Alex A Is there a particular reason you're applying LINCS constraints to your A diamond structure? Usually, LINCS gives convergence A errors/warnings if the system is poorly

Re: [gmx-users] Supercritical CO2

2015-04-30 Thread Alex
appreciate it if you let me know. :) Alex On Thu, Apr 30, 2015 at 2:04 PM, Jarrett Lee Wise jwi...@uwyo.edu wrote: Hello all- I am trying to run simulations containing supercritical CO2 and oil asphaltenes. I have tested various force fields (TraPPE flex, TraPPe rigid, Charmm, EPM2, Cygan

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Alex
sha nedoma...@gmail.com wrote: You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever. Alex Thank you for your reply. I am simulating a PLGA (poly lactic co-glycolic acid molecle). I get the topology file and I solvated the molecule.

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Alex
grompp complaining about in your case. Alex Dear Sir I am using oplsaa force field. In the .rtp file i did not found angles secion for any amino acid. yes there are sections for dihedrals and impropers. sorry for troubling you. Best Anurag Dobhal Juniour Research fellow Supervisor: Dr

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Alex
, or stick them into your ffbonded. Am I missing something here? Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Alex
. :-) Alex On May 4, 2015 11:31 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/4/15 1:06 PM, Alex wrote: JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL required to define connectivity. Remaining bonded interactions are then deduced JL from bond

Re: [gmx-users] Supercritical CO2

2015-05-01 Thread Alex
With opls-aa, incorrect densities and diffusivities were calculated entirely away from the critical point for several liquids. Alex On May 1, 2015 11:40 AM, V.V.Chaban vvcha...@gmail.com wrote: This problem is natural. Even small change in (T,P) in the supercritical range results in a huge

Re: [gmx-users] Supercritical CO2

2015-04-30 Thread Alex
Only other suggestion I have is that 5 ns production runs are probably not long enough. Granted, we needed diffusion data, so I believe I had 50 to 100 ns long simulations, but even for the barostat to settle, it may be a good idea to have simulations significantly longer than 5 ns. Alex On Thu

Re: [gmx-users] Supercritical CO2

2015-05-01 Thread Alex
bond polarity is significantly different in the supercritical state and in the gas state. On Fri, May 1, 2015 at 3:30 PM, Alex nedoma...@gmail.com wrote: I wasn't talking about the initial post. I was talking about the fact that in _very stable_ states the same numerical simulation

Re: [gmx-users] Supercritical CO2

2015-05-01 Thread Alex
I wasn't talking about the initial post. I was talking about the fact that in _very stable_ states the same numerical simulation with a supposedly well-established set of interactions produces garbage. VVC The point is that any metastable state in numerical simulations VVC requires fine-tuned

Re: [gmx-users] Supercritical CO2

2015-05-01 Thread Alex
A cursory search yields: http://www.sciencedirect.com/science/article/pii/0009261496003971# http://www.sciencedirect.com/science/article/pii/S0009261403006407 http://link.springer.com/article/10.1007%2Fs11814-011-0248-5 The first one has some parameters, maybe trying them would be a start. Alex

Re: [gmx-users] Epsilon-rf

2015-04-28 Thread Alex
That's a pretty poorly formed question, including the part where you actually calculate the epsilon-rf value. Can you please try again with a description of your system? Alex MK Dear all, MK I use reaction-field-zero as the coulombtype for my system. I wonder how I MK should choose the right

Re: [gmx-users] Epsilon-rf

2015-04-28 Thread Alex
electrostatics in general. Given the above, I am not sure I understand what's there to calculate, unless you mean running a simulation and _obtaining_ a dielectric property as a result. In that case, given you system, it is a completely different discussion. Alex MK Not a poorly formed but a general

Re: [gmx-users] Epsilon-rf

2015-04-28 Thread Alex
Also, reaction-field-zero, as described here http://manual.gromacs.org/online/mdp_opt.html which _only_ works with epsilon-rf=0. Any particular reason for doing this to your electrostatics? Alex MK Dear all, MK I use reaction-field-zero as the coulombtype for my system. I wonder how I MK

Re: [gmx-users] Epsilon-rf

2015-05-05 Thread Alex
Yup, that should be physically sound. Alex Dear Alex, I have another question related to coulombtype selection. I dont want to use pbc in my system so, PME and Ewald are not good choices. If I use Reaction-field-zero and define a rcoulomb equal to my system size ( since epsilon-rf is 0

Re: [gmx-users] question

2015-05-15 Thread Alex
instructions on where to quickly see what you're talking about would be nice. Once again, this isn't something Gromacs-specific. Alex On May 15, 2015 9:17 AM, Golnaz Roudsari golnaz.c...@gmail.com wrote: Dear gmx-user I want to simulate graphene and surfactants in water. In most of the paper they put

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 87

2015-05-15 Thread Alex
Golnaz, I think you're creating a bit of a mess by replying to the digest. If you don't mind, please see my answer directly to your specific question, where I will also quote your message from below. Alex GR Thank you Alex GR First of all it is better to say that I am a beginner. I follow two

Re: [gmx-users] question

2015-05-15 Thread Alex
, although I only use it as a viewer. There's little to add at this point: learn the tool(s) of your choice and use them to manipulate your coordinates. Alex GR Thank you Alex GR First of all it is better to say that I am a beginner. I follow two papers GR for my project. The authers are ''Tumala

Re: [gmx-users] Carbon Nanotube `Y-Junctions'

2015-05-17 Thread Alex
anything. Alex On Thu, May 14, 2015 at 10:35 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I am looking for XYZ or PDB file of Carbon nanotube ' Y-junction' . I will be grateful if you can let me know how i can find or make it . Thanks in advance .Best

[gmx-users] Pulling a periodic molecule (for the third time)

2015-05-18 Thread Alex
a tarball with the input. Any thoughts? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

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

2015-04-15 Thread Alex
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 s_poora...@yahoo.com wrote: Hi Gromacs users , I want to have a system with one C60 and about 1000 water molecules .I tried

Re: [gmx-users] POPE lipid from Tieleman's web site, the box of xy dimension will shrink during the simulation

2015-04-11 Thread Alex
oscillatory) does not help with long ref_t either, maybe try v-rescale. Alex n Dear all, nI am new to lipid simulation. I have downloaded the pope.pdb, n pope.itp, lipid.itp from Tieleman's web site n (http://wcm.ucalgary.ca/tieleman/downloads). And I have made a n directory named

Re: [gmx-users] How to get the .gro file for MgO surface

2015-04-14 Thread Alex
You probably mean the topology, which you will have to build yourself, likely at the forcefield level. Is there any particular reason for trying to simulate metal oxide with GMX? There are much better tools suited for this, e.g. LAMMPS with ReaxFF. Alex z Dear you, z Does

[gmx-users] R-B dihedrals

2015-04-14 Thread Alex
seen by the system (I tracked the errors to the atomtypes). The dihedral type (3) is listed correctly in the topology. A David Lynch mystery. Any ideas? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] R-B dihedrals

2015-04-14 Thread Alex
GMX issue i've ever had. Alex On Tue, Apr 14, 2015 at 2:38 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Alex, Maybe writing out the preprocessed topology (grompp -pp) or checking the .tpr with gmxdump can show whether the dihedral parameters are really what you think they are. Cheers

Re: [gmx-users] R-B dihedrals

2015-04-14 Thread Alex
Absolutely nothing in between, this is (cos(45)-cos(phi))^2, two minima at 45 and 315 and a peak around 180. Checked if I converted to R-B coefficients correctly -- same thing. At 90/270 clean decrease to 45/315. Alex On Tue, Apr 14, 2015 at 3:16 PM, Justin Lemkul jalem...@vt.edu wrote

Re: [gmx-users] R-B dihedrals

2015-04-14 Thread Alex
Mark, we just figured it out, thanks. :) And yes, you are definitely onto something: two identical dihedrals pulling in opposite directions. This is what happens when people from solid state show up to use GMX. :) Alex On Tue, Apr 14, 2015 at 5:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote

Re: [gmx-users] GMX-compatible DNA coordinates

2015-04-03 Thread Alex
can reveal on a public forum. I hope you'll understand. ;) Alex On Fri, Apr 3, 2015 at 1:33 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Alex, I've done it before, but I can't do it from the top of my head without seeing the input and checking what Gromacs wants. It's not hard work, it's

Re: [gmx-users] Gromacs on Nvidia 830M

2015-04-06 Thread Alex
Of course, it's not CP2K, which will murder your laptop. :) Not for long production simulations, but great for prototyping and shorter tests. Gromacs under Linux is a treat. Alex BP Dear users, BP I perfectly understand that gromacs is not for laptops. However, I was BP wondering about gromacs

[gmx-users] grompp: unknown bond_atomtype

2015-04-01 Thread Alex
is actually opls_335. Gromacs v. 4.6-beta3. Any ideas? Thank you, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] The largest charge group contains [GIANT CRAPTON] of atoms

2015-04-02 Thread Alex
Ah, now I see, thanks. Yes, this entirely follows the paradigm of biomolecules. I still insist that Gromacs was a better choice for my project than LAMMPS. :) On Thu, Apr 2, 2015 at 12:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/2/15 2:28 PM, Alex wrote: Verlet option did remove

Re: [gmx-users] The largest charge group contains [GIANT CRAPTON] of atoms

2015-04-02 Thread Alex
Verlet option did remove that error, thank you. Indeed, there is a large number of atoms with identical cgnr, no idea why. Does it have to do with the order of atoms in your PDB? On Thu, Apr 2, 2015 at 10:22 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/1/15 7:42 PM, Alex wrote: I have

Re: [gmx-users] Setting custom atoms in FF

2015-04-01 Thread Alex
... Thanks for clarifying this, Justin. Kind of a crucial point. Alex On Wed, Apr 1, 2015 at 2:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/1/15 4:24 PM, Alex wrote: That is the issue. I AM using -noparam, and x2top is reverting to an incorrect bond type. Which then sets off errors in grompp

Re: [gmx-users] Setting custom atoms in FF

2015-04-01 Thread Alex
angle function types (within GMX convention). I recall posting a while back about properly parameterizing graphene, and heard mostly meh from the locals (I don't think you participated in that discussion). Alex On Wed, Apr 1, 2015 at 2:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/1/15 4:37

Re: [gmx-users] grompp: unknown bond_atomtype

2015-04-01 Thread Alex
True, true. :) On Wed, Apr 1, 2015 at 2:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/1/15 4:27 PM, Alex wrote: I think I solved it already, thanks. Entirely due to horrible mess created by the necessity to create custom atom types. I wish you guys could make the bond length tolerance

Re: [gmx-users] grompp: unknown bond_atomtype

2015-04-01 Thread Alex
PM, Alex wrote: I am working with a local copy of oplsaa.ff where I have defined a set of custom atom types in atomname2type.n2t and added the bond and angle parameters into ffbonded. x2top creates the topology without issues, but grompp reports a fatal error (see subject). The particular type

Re: [gmx-users] GMX-compatible DNA coordinates

2015-04-03 Thread Alex
Mark, Not to troll, but why did you assume that I didn't do my due diligence before posting here? Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting. Alex Hi, Googling

Re: [gmx-users] cudaStreamSynchronize failed in cu_blockwait_nb

2015-06-08 Thread Alex
-repo-ubuntu1404-7-0-local_7.0-28_amd64.deb, followed by the usual apt-get update/upgrade. Nvcc reports version 7.0.27. GMX version is 5.0.5, locally built, with auto-detected options, including GMX_GPU ON, and GMX_SIMD SSE4.1 On Mon, Jun 8, 2015 at 2:07 PM, Alex nedoma...@gmail.com wrote: Hi all

[gmx-users] cudaStreamSynchronize failed in cu_blockwait_nb

2015-06-08 Thread Alex
is: mdrun -ntomp 4 file directives I saw some previous messages on this error, but not sure there's a solution. Any thoughts? I will provide any additional info as needed. If there are additional options necessary to debug etc, could you provide the exact command line? Thanks, Alex -- Gromacs Users

[gmx-users] GPU acceleration

2015-06-05 Thread Alex
, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

Re: [gmx-users] GPU acceleration

2015-06-05 Thread Alex
Thanks for the info. I tried with GMX_EMULATE_GPU=1 preceding the mdrun line, crashed after 100 steps. Is that the expected behavior? On Fri, Jun 5, 2015 at 2:46 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Fri, Jun 5, 2015 at 10:39 PM, Alex nedoma...@gmail.com wrote: In that case, I am

Re: [gmx-users] GPU acceleration

2015-06-05 Thread Alex
to include those flags, but no recompiling is required. Is that correct? Thanks, Alex On Fri, Jun 5, 2015 at 1:52 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi Alex, That's a quite old CPU so it's hard to tell how fast is it, you'll have to try. There are ways to guesstimate how fast does

Re: [gmx-users] GPU acceleration

2015-06-05 Thread Alex
the system, but for the heck of it... I am now looking at the stats and see that (NxN QSTab + LJ) and (NxN QSTab [F]) take up about 86% of all flops in my simulation. Which of those get offloaded? Thank you, Alex On Fri, Jun 5, 2015 at 2:26 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi Alex

Re: [gmx-users] Microwave

2015-06-07 Thread Alex
? A very necessary field of research, IMO. Alex MA Hi, MA You'd have to contact the authors to get their modified version. MA Mark MA On Sun, Jun 7, 2015 at 11:09 PM Mostafa Javaheri javaheri.grom...@gmail.com MA wrote: Hi all, Thanks for your replies, I searched about the simulation under

Re: [gmx-users] About Pulling code in Gromacs 5.0.2

2015-06-10 Thread Alex
. Steered MD is to be carefully designed. 3. Make sure your boundaries are taken care of properly, in case your pulled object meets the wall. Alex hy Hello all, hy Recently, I preformed a SMD, pulling a nano diamond across the membrane. I hy found that pull_geometry position in the Gromacs 4.6.5

Re: [gmx-users] GPU acceleration

2015-06-09 Thread Alex
yesterday about a fatal error due to CPU-GPU sync issue, but seems like I was able to take care of it. Very impressed here, about to abandon all of my CPU-only runs and switch to the GPU node as my workhorse. Alex On Tue, Jun 9, 2015 at 3:43 PM, Szilárd Páll pall.szil...@gmail.com wrote

Re: [gmx-users] GPU acceleration

2015-06-09 Thread Alex
concern is cooling. Comments highly appreciated. Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] constraint pull code / gromacs 5.0.4

2015-06-23 Thread Alex
...which is correct if one is sampling independent windows and collecting the forces to reconstruct the PMF. That is nominally true, but if there are weird COM motions (due to something seriously wrong in the system), the puller could further shake things up -- I have seen this in my own

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