Re: [gmx-users] Fwd: Static compilation of gromacs

I know, but on target machine there is a gcc compilator version 4.1, and on gromacs site they told that this version is broken and 4.5 should used instead. So I try to compile it on machine with 4.5 version of gcc 2013/5/15 Alexey Shvetsov > В письме от 15 мая 2013 00:11:49 пользователь Андрей

Re: [gmx-users] Fwd: electrostatic potential map

Thanks I have little more confusion about the charges assigned to each of the atoms from pdb2pqr. With and without water the charges of all the protein atoms are same! But, then why this type of discrepancy is coming from the potential map? Thanks for giving the apbs mailing list address. I'll pos

Re: [gmx-users] g_dist problem in Implicit solvent

On 5/14/13 7:26 PM, Tong Li wrote: Dear All, I got this problem recently. I want to use g_dist to calculate the distance between two group in my simulation system. However, when I use the implicit solvent for simulation, g_dist went into this problem: Molecule in topology has atom numbers b

[gmx-users] g_dist problem in Implicit solvent

Dear All, I got this problem recently. I want to use g_dist to calculate the distance between two group in my simulation system. However, when I use the implicit solvent for simulation, g_dist went into this problem: Molecule in topology has atom numbers below and above natoms. I have used tpb

[gmx-users] FW:

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Re: [gmx-users] Fwd: Static compilation of gromacs

В письме от 15 мая 2013 00:11:49 пользователь Андрей Гончар написал: > Hi. I'm trying to static compile gromacs from source, everything goes well, > but when I > move it to another machine and try to launch mdrun I got a message: > > mdrun: error while loading shared libraries: libfftw3f.so.3: can

[gmx-users] Usage of g_spatial

Sounds like a trjconv problem, not a g_spatial problem to me. You should center only the group that makes sense for your SDF -- you probably want to pick a single cation for this (then, separately, do another run selecting a single anion; each will be used to generate a separate SDF). Then outp

[gmx-users] Fwd: Static compilation of gromacs

Hi. I'm trying to static compile gromacs from source, everything goes well, but when I move it to another machine and try to launch mdrun I got a message: mdrun: error while loading shared libraries: libfftw3f.so.3: cannot open shared object file: No such file or directory I run ./configure with

Re: [gmx-users] Fwd: electrostatic potential map

Tarak, That's more of a question for the APBS mailing list, but I'll give it my best shot, but I would highly suggest you check out http://www.poissonboltzmann.org/apbs first. APBS is an implicit solvent electrostatics model, and as such you should be careful with what explicit solvent you includ

Re: [gmx-users] numbering after 99999SOL

>> Gromacs do not use residue number or atom number, OK! Thanks Nuno and Mark regards, On Tue, May 14, 2013 at 7:14 PM, Mark Abraham wrote: > Try selecting residue 0 with editconf and see for yourself :-) > On May 14, 2013 4:41 PM, "gromacs query" wrote: > > > Dear Nuno, > > > > I used gencon

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Sure - I added the input files to the Redmine issue. Reza On May 14, 2013, at 9:21 AM, David van der Spoel wrote: > On 2013-05-13 21:57, Reza wrote: >> So I think I figured out what was causing the discrepancy of Charmm27 >> energies between gromacs and NAMD. It appears that it's related to th

Re: [gmx-users] Re: QM/MM simulations

On 5/14/13 12:07 PM, DavidPO wrote: Thank for your answer. But it change nothing. To tell the truth, I rather young user of linux. May be it is the problem with flags? I can't be sure, that I did all right. Neither can we, unless you provide us with exactly what you did and what the outpu

Re: [gmx-users] g_sgangle and P atoms on the DNA molecule.

On 5/14/13 10:25 AM, anna_grom...@libero.it wrote: Dear all, in referring to the described probelm with g_sgagle results, I would like to add the following: I made an index file like this: 0 System : 762 atoms 1 DNA : 762 atoms 2 a_412_444 : 2 at

Re: [gmx-users] numbering after 99999SOL

Try selecting residue 0 with editconf and see for yourself :-) On May 14, 2013 4:41 PM, "gromacs query" wrote: > Dear Nuno, > > I used genconf -f del.gro -o del.g96 > > Again it gives max of 9 then starts with 0; sample shown here > > del.g96 > > 9 SOL OW332114 13.572541.9

Re: [gmx-users] lincs errors late in simulation

I wouldn't call 8ps "late." Since you probably don't know how large a time step is safe, I'd try 0.1 fs for equilibration, and raise it later if it proves stable. Mark On May 14, 2013 4:28 PM, "Joe Smerdon" wrote: > > Hi all, > > First of all I'm new to md simulations, so if I am missing anythin

Re: [gmx-users] lincs errors late in simulation

On 5/14/13 10:27 AM, Joe Smerdon wrote: Hi all, First of all I'm new to md simulations, so if I am missing anything simple, I would be grateful for any pointers, however small. I am trying to simulate many small molecules on a substrate. I am restraining my substrate from moving but allo

Re: [gmx-users] range angle calculated by g_sgangle

On 5/14/13 11:03 AM, battis...@libero.it wrote: Dear users and experts, why the angle calculated by g_sgangle, that are given in degrees, are only in the range (-1, 1)? The format of g_sgangle is time, cos(angle), angle. Since values of cos(angle) are within { -1, 1 } that explains what

[gmx-users] Re: QM/MM simulations

Thank for your answer. But it change nothing. To tell the truth, I rather young user of linux. May be it is the problem with flags? I can't be sure, that I did all right. Best regards, David -- View this message in context: http://gromacs.5086.x6.nabble.com/QM-MM-simulations-tp5008196p50082

Re: [gmx-users] do_dssp

On 5/14/13 11:11 AM, Xu Dong Huang wrote: Preeti, if do_dssp doesn't work for you, try to do it manually using the following web service: http://www.cmbi.ru.nl/hsspsoap/ I use it because my platform (MAC OSX) can't run DO_DSSP I've used dssp/do_dssp on Mac for years. It's all a matter of

Re: [gmx-users] Fwd: do_dssp

On 5/14/13 11:03 AM, Preeti Choudhary wrote: -- Forwarded message -- From: Preeti Choudhary Date: Tue, May 14, 2013 at 8:30 PM Subject: do_dssp To: Discussion list for GROMACS users I am facing problem while using do_dssp.I need to store secondary structure data every 100 ps

Re: [gmx-users] g_cluster warning

Hi, I don't know. I don't know how to trigger it, and nobody has said how they triggered it :-) Mark On May 14, 2013 4:45 PM, "Preeti Choudhary" < preetichoudhary18111...@gmail.com> wrote: > should we worry about the warning ??? > > > On Tue, May 14, 2013 at 7:19 PM, Mark Abraham >wrote: > > >

Re: [gmx-users] do_dssp

Preeti, if do_dssp doesn't work for you, try to do it manually using the following web service: http://www.cmbi.ru.nl/hsspsoap/ I use it because my platform (MAC OSX) can't run DO_DSSP Best of luck! On May 14, 2013, at 11:00 AM, Preeti Choudhary wrote: > I am facing problem while using do

Re: [gmx-users] numbering after 99999SOL

I'm sorry. I get confused with residue number and atom number. For the analysis and other Gromacs tools, you will need a index file. Gromacs do not use residue number or atom number, so it's not a problem to have two or more residues with the same residue number. Nuno -- gmx-users mailing list

[gmx-users] range angle calculated by g_sgangle

Dear users and experts, why the angle calculated by g_sgangle, that are given in degrees, are only in the range (-1, 1)? Many thanks, Anna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs

[gmx-users] Fwd: do_dssp

-- Forwarded message -- From: Preeti Choudhary Date: Tue, May 14, 2013 at 8:30 PM Subject: do_dssp To: Discussion list for GROMACS users I am facing problem while using do_dssp.I need to store secondary structure data every 100 ps.For this I am using -dt option.But I didn't get

[gmx-users] do_dssp

I am facing problem while using do_dssp.I -- 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 lis

Re: [gmx-users] g_cluster warning

should we worry about the warning ??? On Tue, May 14, 2013 at 7:19 PM, Mark Abraham wrote: > We'd need a lot more info to start to understand why .tpr vs .gro > does/should affect the result (or not)! > > Mark > On May 14, 2013 2:32 PM, "Sabine Reisser" wrote: > > > Hi, > > > > I'm having the s

Re: [gmx-users] numbering after 99999SOL

Dear Nuno, I used genconf -f del.gro -o del.g96 Again it gives max of 9 then starts with 0; sample shown here del.g96 9 SOL OW332114 13.572541.92599 13.545999527 9 SOL HW1 332115 13.4919996261.92746 13.60492 9 SOL HW2 332116 13.576

[gmx-users] lincs errors late in simulation

Hi all, First of all I'm new to md simulations, so if I am missing anything simple, I would be grateful for any pointers, however small. I am trying to simulate many small molecules on a substrate. I am restraining my substrate from moving but allowing the molecules to do whatever they like.

[gmx-users] g_sgangle and P atoms on the DNA molecule.

Dear all, in referring to the described probelm with g_sgagle results, I would like to add the following: I made an index file like this: 0 System : 762 atoms 1 DNA : 762 atoms 2 a_412_444 : 2 atoms 3 a_444_474 : 2 atoms with:g_sgangle

Re: [gmx-users] numbering after 99999SOL

I'm guessing that you are using .gro file format. That's a limitation of the file format. See http://manual.gromacs.org/online/gro.html If you really need different residue number for each residue, use .g96 file format instead. Cheers Nuno Azoia On Tue, May 14, 2013 at 3:08 PM, gromacs query w

[gmx-users] numbering after 99999SOL

Dear All, I have a huge system and residue number goes beyond 9. So when I added waters then residue number goes till 9SOL then again it starts from 0SOL. I tried genconf -renumber option but it does not help. Though it can be done with small scripting, just want to know if it can be done

Re: [gmx-users] g_cluster warning

We'd need a lot more info to start to understand why .tpr vs .gro does/should affect the result (or not)! Mark On May 14, 2013 2:32 PM, "Sabine Reisser" wrote: > Hi, > > I'm having the same warning, would also be interested in what it means. > > Additionally, I get different results if I use a t

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

On 2013-05-13 21:57, Reza wrote: So I think I figured out what was causing the discrepancy of Charmm27 energies between gromacs and NAMD. It appears that it's related to the gromacs version: energies from 4.5.7 and NAMD match very well while 4.6.1 gives energies that are different from both 4.

[gmx-users] g_sgangle and P atoms on the DNA molecule.

Dear users and experts, my question is about the results given by the program g_sgangle, when I try to calculate the angles between the two vectors defined by 3 consecutive P atoms, on the DNA structure (a single gro structure), the result is: @title "Angle between a_728_695 and a_695_662

Re: [gmx-users] g_cluster warning

Hi, I'm having the same warning, would also be interested in what it means. Additionally, I get different results if I use a tpr instead of a gro file in the -s option, using the same trajectory with -f. The results are completely different, for the gro file I get 42 while for the tpr file I

[gmx-users] 'the reciprocal space calculation will not necessarily cancel'

Hi, I'm not clear on the meaning and implications of this warning message from grompp: WARNING 1 [file ../md.mdp]:   With coulomb soft core, the reciprocal space calculation will not   necessarily cancel.  It may be necessary to decrease the reciprocal space   energy, and increase the cutoff ra

Aw: Re: [gmx-users] air-water-interface

I was under the impression a vacumn, or even gas/liquid interface becomes uniform molecule wise in such simulations due to scale.  Thus, the applied pressure and other corrections necessary to set up the interface on a small scale, such as caclulated force at an imaginary interface for given gas/li

Re: [gmx-users] setting up a simulation of an ionic liquid

Yes, I am running NpT with Berendsen coupling. So far I have just dealt with neat ILs, so I have no experience with water. But as Justin mentioned, do not change the parameters given by the FF, which can really introduce strange artefacts, e.g too high or too low density, dynamics, ... Cheers, F

RE: [gmx-users] setting up a simulation of an ionic liquid

Thanks for the help Flo, At step 3 are you running NPT? Out of interest do you have any water in the box? If so which model are you using for the water? Laura From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Florian Domme

Re: [Spam:*****] [gmx-users] REMD analysis

The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta wrote: > Dear

Re: [gmx-users] setting up a simulation of an ionic liquid

Hi, perhaps try for the first 1000-10 steps to set nstlist=1. I also had very much trouble with setting up IL systems, but now I have the following routine: 1. use genbox to fit the cations and anions in a large box 2. energy minimization 3. run with nstlist=1, perhaps even particle deco

RE: [gmx-users] setting up a simulation of an ionic liquid

Thanks for the help Justin, I've taken a look at the atom with the maximum force using VMD and I can't see anything wrong with it. Its part of a whole molecule and not particularly close to any other molecules either. I suspect I may need to take another look at the force field but want to make

Re: [gmx-users] Large number of solvent molecules

Well, a linear 80aa peptide will need that much water anyways! The question is more how relevant and realistic is such a structure and how long the peptide is going to keep it? You could resolvate it after some time, reducing the box, you could also start by a vacuo simulation to help colapse

Re: [gmx-users] Large number of solvent molecules

Hi, Have a look at the following article. It describes a non-standard box type that seems ideal for your application. I don't know what is the latest gromacs version where it is implemented, however. Author = {Wassenaar, TA and Mark, AE}, Title = {{The effect of box shape on the dynamic propert