[gmx-users] R: problem with .edr file

Dear Berk, probably I was not able to explain correctly my problem. I can assure you that the problem with .edr file exists, and that using that .edr file I'm not able to create graphs in which I can see the behaviour of the energy as I usually did in other simulations. To be more clear, I'm pastin

[gmx-users] Regular vs. CHARMM TIP3P water model

Hello everybody, I have many difficulties to reproduce TIP3P simulation results with CHARMM TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM counterpart, independantly from the cutoff for non-bonded interactions, the version of GROMACS (4.5.1 or 4.0.7) or the double precis

Re: [gmx-users] Regular vs. CHARMM TIP3P water model

On 2010-09-14 10.23, Nicolas SAPAY wrote: Hello everybody, I have many difficulties to reproduce TIP3P simulation results with CHARMM TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM counterpart, independantly from the cutoff for non-bonded interactions, the version of G

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

Hi, I don't understand what exactly you want to reproduce. Standard tip3p and Charmm tip3p are different models, so the density does not have to be identical. The Gromacs Charmm FF implementation paper: http://pubs.acs.org/doi/full/10.1021/ct900549r gives 1002 for tip3p and 1015 for charmm tip3p

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

Hi, We did some checking. The value of the density for tip3p reported in the Gromacs Charmm ff implementation of 1001.7 is incorrect. This should have been 985.7. The number of 1014.7 for Charmm tip3p is correct. I would expect that the difference with your number is mainly due to the shorter

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

Hi, My last comment was not correct. Sorry, too many numbers in my head. Both your density numbers are too low, more than can be explained by LJ cut-off settings. How did you determine the density? g_density does not give the correct number. The number in our paper for tip3p (not Charmm tip3p)

Re: [gmx-users] Correction for the PBC!

tekle...@ualberta.ca wrote: Dear Justine, I just checked at the archive list and found out lots of information on how to correct for PBC! And if I understood it correctly is this the right way to follow... “If you are trying to correct for periodicity for all species in the system (protein

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

> > Hi, > > I don't understand what exactly you want to reproduce. > Standard tip3p and Charmm tip3p are different models, so the density does > not have to be identical. > The Gromacs Charmm FF implementation paper: > http://pubs.acs.org/doi/full/10.1021/ct900549r > gives 1002 for tip3p and 1015 f

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

> > Hi, > > My last comment was not correct. Sorry, too many numbers in my head. > Both your density numbers are too low, more than can be explained by LJ > cut-off settings. > > How did you determine the density? > g_density does not give the correct number. The number in our paper for > tip3p (n

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

> Date: Tue, 14 Sep 2010 13:11:47 +0200 > Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model > From: nicolas.sa...@cermav.cnrs.fr > To: gmx-users@gromacs.org > > > > > Hi, > > > > I don't understand what exactly you want to reproduce. > > Standard tip3p and Charmm tip3p are different

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

Hi, The choice of constraint algorithm is irrelevant for the results. As I understood Charmm tip3p has less structure than standard tip3p and it would not surprise me if the density is different. But I have never closely looked at Charmm tip3p properties myself. Berk > Date: Tue, 14 Sep 2010 1

[gmx-users] SWM4-NDP water model in GROMACS

Dear gromacs users, Does anyone have experience in implementation of polarizable SWM4-NDP water model by Lamoureux et al. (Chem.Phys.Lett. 418,245 (2006)) in gromacs? I have performed several simulations with systems of different size (from 1024 up to 8192 water molecules) with dispersion corr

[gmx-users] g_helix problem

Dear Gromacs Users: I have a problem when I try to run g_helix in Gromacs 4.0.5. I have two systems, each one containing a peptide, both with the same number of aminoacids; however, in one of them, most of the AA residues are not usual (in fact, they are post-translationally modified; thus, to

[gmx-users] xpm2ps failure - memory allocation

Hi All, I'm having a problem with xpm2ps failing in both version 4.5 and the current git version (pulled just a few minutes ago). The program exits with: xpm2ps(24704) malloc: *** error for object 0x803201: pointer being reallocated was not allocated *** set a breakpoint in malloc_error_br

[gmx-users] an example to test mdrun-gpu x mdrun

Hi there, I am testing on a MBP 17" SL 10.6.4 64 bits and nvidia GeForce 9600M GT So I got mdrun-gpu compiled and apparently running, but when I try to run 'mdrun' to compare I have a segment fault. Any other comments to the md.mdp and em.mdp are very welcome too. # To test mdrun-gpu cat <

Re: [gmx-users] xpm2ps failure - memory allocation

On 2010-09-14 15.12, Justin A. Lemkul wrote: Hi All, I'm having a problem with xpm2ps failing in both version 4.5 and the current git version (pulled just a few minutes ago). The program exits with: xpm2ps(24704) malloc: *** error for object 0x803201: pointer being reallocated was not allocate

RE: [gmx-users] xpm2ps failure - memory allocation

Hi, There were several issues which I fixed. But my test file/system did not give problems with the buggy code. Could you test it on your system (use release-4-5-patches)? Thanks, > Date: Tue, 14 Sep 2010 09:12:18 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: [gmx-users]

Re: [gmx-users] xpm2ps failure - memory allocation

David van der Spoel wrote: On 2010-09-14 15.12, Justin A. Lemkul wrote: Hi All, I'm having a problem with xpm2ps failing in both version 4.5 and the current git version (pulled just a few minutes ago). The program exits with: xpm2ps(24704) malloc: *** error for object 0x803201: pointer bein

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

> > Hi, > > We did some checking. > The value of the density for tip3p reported in the Gromacs Charmm ff > implementation of 1001.7 is incorrect. > This should have been 985.7. The number of 1014.7 for Charmm tip3p is > correct. I have just done a quick test using dispersion correction (DispCorr=

Re: [gmx-users] Correction for the PBC!

Dear Justine, No, I have 20 surfactants in my system in a pure solvent and try to see the aggregation and adsorption properties of these molecules. I have run them for 20ns. And now start to analyze my data. Just in short I want to correct for periodicity! so that to get the accurate resul

Re: [gmx-users] Correction for the PBC!

tekle...@ualberta.ca wrote: Dear Justine, No, I have 20 surfactants in my system in a pure solvent and try to see the aggregation and adsorption properties of these molecules. I have run them for 20ns. And now start to analyze my data. Just in short I want to correct for periodicity! so

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

Good. I just calculated tip3p energies for a Charmm tip3p trajectory. Standard tip3p gives 1.1 kJ/mol per water molecule higher energies. Thus the LJ on H's gives significant extra attraction which increases the density. Berk > Date: Tue, 14 Sep 2010 15:49:03 +0200 > Subject: RE: [gmx-users] R

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

> > Good. > > I just calculated tip3p energies for a Charmm tip3p trajectory. > Standard tip3p gives 1.1 kJ/mol per water molecule higher energies. > Thus the LJ on H's gives significant extra attraction which increases the > density. Great, I obtain a similar result: -40.0 kJ/mol for regular tip

Re: [gmx-users] Regular vs. CHARMM TIP3P water model

On 2010-09-14 17.06, Nicolas SAPAY wrote: Good. I just calculated tip3p energies for a Charmm tip3p trajectory. Standard tip3p gives 1.1 kJ/mol per water molecule higher energies. Thus the LJ on H's gives significant extra attraction which increases the density. Great, I obtain a similar re

[gmx-users] compilation problem: gromacs 4.5 double precision

Hi all. I have a problem building the double (but not single) precision version of gromacs 4.5 on an AMD "instanbul" based system. compiler is gcc3.4, configure line: ./configure --prefix=/home/gromacs451 -program-suffix=_d --disable-float --enable-double and the error: In file included from n

Re: [gmx-users] compilation problem: gromacs 4.5 double precision

Hi David, Are you sure you're using gcc 3.4? Because if you are, I'd strongly suggest that you switch to 4.x! Cheers, -- Szilárd On Tue, Sep 14, 2010 at 5:21 PM, David Parcej wrote: > Hi all. > I have a problem building the double (but not single) precision version of > gromacs 4.5 on an AMD

Re: [gmx-users] FEP top file setup...

Ok I think I know where you are going with this. I started a small 2 nucleic acid system. I set RNA_Chain_A as the couple-moltype and couple-lambda0 and couple-lambda1 to vdw-q and none respectively. I then began a steep mdrun and got this error:     Program mdrun,

Re: [gmx-users] Correction for the PBC!

Dear Justine, I have tried every thing but the g_rdf of my surfactant molecules Surfactant = PAP PAP-PAP .. RDF looks like this.. 00 0.002 0 0.004 0 0.006 0 0.008 0 0.01 0 0.012 0 0.

Re: [gmx-users] Correction for the PBC!

tekle...@ualberta.ca wrote: Dear Justine, I have tried every thing but the g_rdf of my surfactant molecules Surfactant = PAP PAP-PAP .. RDF looks like this.. 00 0.002 0 0.004 0 0.006 0 0.008 0 0.01

Re: [gmx-users] Units of k1 in the pulling code

Dear Berk: Thank you so much for the clarification!!! It is so helpful! Best! Xueming On Fri, Aug 13, 2010 at 4:13 AM, Berk Hess wrote: > > > > Date: Thu, 12 Aug 2010 17:33:09 -0400 > > From: chris.ne...@utoronto.ca > > To: gmx-users@gromacs.org > > Subject: [gmx-users] Units of k1 in the pull

Re: [gmx-users] Units of k1 in the pulling code

Dear Chris: Thank you very much for it! Best! Xueming On Thu, Aug 12, 2010 at 5:33 PM, wrote: > Dear Xueming: > > the word "mol" is short form for "mole" > > http://en.wikipedia.org/wiki/Mole_%28unit%29 > > In the pull code context, it refers to moles of the pulled group. > > The force is not

[gmx-users] Amb2gmx

Dear all, Lennard Jones radius parameters are converted between gromacs and amber with the conversion factor (2**(5/6))/10 in the amb2gmx script. While I understand that the 10 takes care of the Angstrom to nanometers conversion I do not understand the origin of the 2 to the power of 5/6. I wou

[gmx-users] Fw: NO GSL! Can't find and take away ballistic term in ACF without GSL

--- On Tue, 9/14/10, Yao Yao wrote: Dear Gmxers, > I met this msg when running g_hbond > in 4.5-beta version. > Then it gives "Segmentation Fault" without any time frame > reading. > Does anyone know what it means? > > thanks, Yao >       > -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] NO GSL! Can't find and take away ballistic term in ACF without GSL

Yao Yao wrote: I met this msg when running g_hbond in 4.5-beta version. Then it gives "Segmentation Fault" without any time frame reading. Does anyone know what it means? I presume from your subject line that you received an additional error message. It indicates that you did not compile

[gmx-users] NO GSL! Can't find and take away ballistic term in ACF without GSL

I met this msg when running g_hbond in 4.5-beta version. Then it gives "Segmentation Fault" without any time frame reading. Does anyone know what it means? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

RE: [gmx-users] how to let the grompp finding libraryfromworkingdirectory first.

For future reference, if someone has a similar problem, would be a good idea to actually state what the issue you had was, and how you fixed it. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Pa

Re: [gmx-users] Solvent Accessible Surface area (SASA) graph label

eyem noob wrote: Dear all, I am having a doubt that the Solvent Accessible Surface area (SASA) graph is having a mistake on the label of hydrophilic and hydrophobic plot? because I get a weird result from the plot... If you want any useful advice, you'll have to do a whole lot better

[gmx-users] Solvent Accessible Surface area (SASA) graph label

Dear all, I am having a doubt that the Solvent Accessible Surface area (SASA) graph is having a mistake on the label of hydrophilic and hydrophobic plot? because I get a weird result from the plot... g_sas analysis was done by GROMACS v3.3 thanks

[gmx-users] Having Multiple Chains From One pdb File

Hi, I have a pdb file with a single short peptide chain. I would like to simulate multiple chains, in this case 5. I've looked at: http://www.gromacs.org/Documentation/How-tos/Multiple_Chains but am still a little confused. Is it possible to get more detail on how to simulate multiple cha

[gmx-users] Output per-group kinetic energy

Dear All, I want to do something very simple: output, say, the kinetic energies for a subset of my system. For example some energy group of my system. Is this possible? Creating an index file, and listing each group as an energy group in my mdp file doesn't get this data into the energy file, only

Re: [gmx-users] Having Multiple Chains From One pdb File

C Johnson wrote: Hi, I have a pdb file with a single short peptide chain. I would like to simulate multiple chains, in this case 5. I've looked at: http://www.gromacs.org/Documentation/How-tos/Multiple_Chains but am still a little confused. Is it possible to get more detail on how to s

Re: [gmx-users] Output per-group kinetic energy

Anthony Costa wrote: Dear All, I want to do something very simple: output, say, the kinetic energies for a subset of my system. For example some energy group of my system. Is this possible? Creating an index file, and listing each group as an energy group in my mdp file doesn't get this data i

[gmx-users] reg grompp error in QM/MM of mopac gromacs

Dear sir/Madam  thanks in Advance     i wanted to do QM/MM for simple peptide .i have edited my topology files as given in the manual i also include the Link atom(LA) under [DUMMIES2] secction of my topology  .but when i run the following grompp command ./grompp_d  -f em.mdp -

[gmx-users] Re: Dear Dr.Van Der Spoel

On 2010-09-14 22.27, mohsen ramezanpour wrote: Dear Dr.Van Der Spoel I want to calculate binding fre energy between proteins and drugs. does Gromacs change protonation state of protein and drug itself when I fill my simulating box with solute? Or I need to use some server as PROPKA to predict and

[gmx-users] reg grompp error for QM/MM setup

Dear sir/Madam  thanks in Advance     i wanted to do QM/MM for simple peptide .i have edited my topology files as given in the manual i also include the Link atom(LA) under [DUMMIES2] secction of my topology  .but when i run the following grompp command ./grompp_d  -f em.md

Re: [gmx-users] reg grompp error in QM/MM of mopac gromacs

- Original Message - From: vidhya sankar Date: Wednesday, September 15, 2010 16:22 Subject: [gmx-users] reg grompp error in QM/MM of mopac gromacs To: gmx-users@gromacs.org --- | > Dear sir/Madam thanks in Advance >

Re: [gmx-users] reg grompp error in QM/MM of mopac gromacs

On 2010-09-15 07.55, vidhya sankar wrote: Dear sir/Madam thanks in Advance i wanted to do QM/MM for simple peptide .i have edited my topology files as given in the manual i also include the Link atom(LA) under [DUMMIES2] secction of my topology .but when i run the following grompp command ./grom