Re: [gmx-users] diff behaviour from same .tpr file under v3.3 /3.3.2

Paul Rowntree wrote: Greetings All; I have reinstalled my Rocks cluster which went from CentOs4 to CentOs5 . I downloaded the Gromacs 3.3.2 RPMs, and although the examples work fine, my own simulations (surface tethered species, OPLS-AA) are blowing up, even though they are minimized as usual

[gmx-users] diff behaviour from same .tpr file under v3.3 /3.3.2

Greetings All; I have reinstalled my Rocks cluster which went from CentOs4 to CentOs5 . I downloaded the Gromacs 3.3.2 RPMs, and although the examples work fine, my own simulations (surface tethered species, OPLS-AA) are blowing up, even though they are minimized as usual. I see no differences

Re: [gmx-users] grompp in gromacs-4.0.4

S. Vaitheeswaran wrote: Dear gromacs users, I am trying to calculate the PMF along the end-to-end distance for a short polymer (hexa-ethylene glycol), using the pull code in gromacs-4.0.4. I run grompp with: grompp_s -v -n OH_ends.ndx -f sd.mdp -c 0.425nm.pdb -p 6EG.top, where sd.mdp is:

[gmx-users] grompp in gromacs-4.0.4

Dear gromacs users, I am trying to calculate the PMF along the end-to-end distance for a short polymer (hexa-ethylene glycol), using the pull code in gromacs-4.0.4. I run grompp with: grompp_s -v -n OH_ends.ndx -f sd.mdp -c 0.425nm.pdb -p 6EG.top, where sd.mdp is: title

Re: [gmx-users] Some molecules disconnected into many parts after EM

Dear Justin: Sorry to bother so many times. After EM everything looks fine. However the mdrun died with the error: --- Program mdrun_d, VERSION 4.0.4 Source code file: gmx_fft_mkl.c, line: 825 Fatal error: Error executing Intel MKL FFT. ---

RE: [gmx-users] make install-mdrun

Thanks Justin. I thought by default everything should be in downloads. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: May 8, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-user

Re: [gmx-users] Some molecules disconnected into many parts after EM

VMD guesses bonds based on distances, so it is not necessarily very smart. I have no idea why increasing the box causes the molecules to be displayed correctly, other than that VMD cannot deal with the periodicity correctly, as I implied before. Causing all of the molecules to be within the u

Re: [gmx-users] make install-mdrun

Payman Pirzadeh wrote: Thanks Diego, But, the latest I found on downloads of gromcs webpage was 4.0.3! Is 4.0.4 somewhere else? The homepage and wiki both have the links to 4.0.4, or you can simply change the ftp link to point to gromacs-4.0.4 instead of 4.0.3. -Justin Payman *F

[gmx-users] Test-set

Thanks, Justin. Then does it mean I cannot use the program to do simulation at this point? any suggestion on it? Johnny Date: Fri, 08 May 2009 12:31:31 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Test-set To: Discussion list for GROMACS users Message-ID: <4a045e63.1080...@vt.edu>

Re: [gmx-users] Some molecules disconnected into many parts after EM

Dear Justin: Thanks for your message. When I open the gro file using VMD it shows: atom:1950 bonds 1907 residue:43 I was thinking the problem may not come from the artifact of visualization. Since if the gro file is fine it should be like: atom:1950 bonds 1944 residue:6 because I have 6 chain

RE: [gmx-users] make install-mdrun

Thanks Diego, But, the latest I found on downloads of gromcs webpage was 4.0.3! Is 4.0.4 somewhere else? Payman From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Diego Enry Gomes Sent: May 8, 2009 11:27 AM To: Discussion list for GROMACS users Subject

Re: [gmx-users] make install-mdrun

get gromacs 4.04 Confirm if you changed the permissions correctly and can write anywhere in /usr/local/ Are you doing this as 'root' or super user (sudo) ? Because if you are just a regular user, will won't be able to change the permissions in /usr/local/. So, configure gmx to be install

[gmx-users] make install-mdrun

Hi All, I realized that I am missing (Lib and bin folders) analysis tools and mdrun MPI. I re-installed the GROMACS 4.0.3, and I found that when I get to 'make install-mdrun' the following messages show up ( I am just copying last lines): make[2]: *** [install-libLTLIBRARIES] Error 1 make[2]:

[gmx-users] Re: gmx-users Digest, Vol 61, Issue 31

Yes, 4.0.4. I know topolbuild well, but I've been working on application (acpypi) that is essentially python interface for antechamber with "steroids" and able to generate topol files for GMX with AMBER99SB/GAFF parameters. I've doing some tests with the possibility of generating OPLS/AA as well.

Re: [gmx-users] Test-set

Zhanglin Ni wrote: The configurations are Linux version 2.6.27.21-170.2.56.fc10.i686.PAE (gcc version 4.3.2 20081105 (Red Hat 4.3.2-7) (GCC) ) #1 SMP Mon Mar 23 23:24:26 EDT 2009 CPU1: Intel(R) Core(TM)2 Duo CPU E7400 @ 2.80GHz stepping 0a lspci 00:00.0 Host bridge: Intel Corporation 82G

[gmx-users] Test-set

The configurations are Linux version 2.6.27.21-170.2.56.fc10.i686.PAE (gcc version 4.3.2 20081105 (Red Hat 4.3.2-7) (GCC) ) #1 SMP Mon Mar 23 23:24:26 EDT 2009 CPU1: Intel(R) Core(TM)2 Duo CPU E7400 @ 2.80GHz stepping 0a lspci 00:00.0 Host bridge: Intel Corporation 82G33/G31/P35/P31 Express

Re: [gmx-users] Problem with protein in lipid bilayer simulation

Anirban Ghosh wrote: Hi ALL, I am trying to run a simulation of a GPCR protein in a POPC bilayer. I have got the lipid.itp file and trying to use the ffgmxbon.itp and ffgmxnb.itp for the simulation. I am getting errors like "LC3 atom not found", "HC atom not found" after incorporating sever

Re: [gmx-users] updated OPLS/AA

Alan skrev: Can someone confirm that GMX 4.x is already released with updated OPLS/AA files as once mentioned in http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,7/Itemid,26/ ? Yes. It has been possible to use OPLS-AA in GROMACS for a long time. Kind regards Andreas

[gmx-users] Problem with protein in lipid bilayer simulation

Hi ALL, I am trying to run a simulation of a GPCR protein in a POPC bilayer. I have got the lipid.itp file and trying to use the ffgmxbon.itp and ffgmxnb.itp for the simulation. I am getting errors like "LC3 atom not found", "HC atom not found" after incorporating several changes in the itp fil

Re: [gmx-users] x2top taking too long

Justin A. Lemkul wrote: Is this version 4.0.4? I get the same thing under the newest version. I think x2top fluctuates in terms of its level of usability, since it is in an ongoing state of development. Older versions (i.e., 3.3.3) should work, at least in terms of generating a basic topol

Re: [gmx-users] x2top taking too long

Is this version 4.0.4? I get the same thing under the newest version. I think x2top fluctuates in terms of its level of usability, since it is in an ongoing state of development. Older versions (i.e., 3.3.3) should work, at least in terms of generating a basic topology. -Justin Alan wrot

[gmx-users] x2top taking too long

Hi there, So I decided to give a try with x2top. x2top -f aaa.gro -o aaa.top However, the program starts and seems to never finishing holding as: [snip] There are 23 name to type translations Generating bonds from distances... atom 0 And 'atom 0' stays there while I clearly see my cpu running w

Re: [gmx-users] how to use atom2cg.awk

xi zhao wrote: Dear Sirs: I wang to know simulate coarse-graied system using gromacs, but I don not know how to use atom2cg.awk to convert CG model! Thank you very much! ./atom2cg_v2.1_tryout.awk my.pdb > out.pdb Note that the script available online needs to be modified to include a

Re: [gmx-users] (no subject)

Antonia V. wrote: Please use a descriptive subject line and reply quoting the previous message. It's not your reader's job to work out your context if you're the one asking for free help! Unfortunately, it' s the only way I can do it, since I want two completely separated phases. I have no

[gmx-users] (no subject)

Unfortunately, it' s the only way I can do it, since I want two completely separated phases. With the tools provided by GROMACS I get a mixture, is there a way to get a box with two separated phases? Antonia _ Show them the way!

Re: [gmx-users] (no subject)

Antonia V. wrote: Hi, I just put one box on top of the other in order to make my new system. I use no constraints for the system, and I can't figure out the problem. It seems that the water molecules of the new system are getting crazy... Unfortunately, "on top" is also not a helpful descript

FW: [gmx-users] (no subject)

> Date: Fri, 8 May 2009 19:38:41 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] (no subject) > > Antonia V. wrote: > > Dear all, > > > > I am trying to simulate a water-liquid crystal system. My initial is box > > is creating by merging two well e

[gmx-users] Re: gmx-users Digest, Vol 61, Issue 29

ntly 3.3.3, but I'm actually going to use > 4.x. for this once I know how to use x2top properly. > > Thanks in advance, > Vasilii > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090508/8b33

[gmx-users] (no subject)

Hi, I just put one box on top of the other in order to make my new system. I use no constraints for the system, and I can't figure out the problem. It seems that the water molecules of the new system are getting crazy... Antonia _

Re: [gmx-users] (no subject)

Antonia V. wrote: Dear all, I am trying to simulate a water-liquid crystal system. My initial is box is creating by merging two well equilibrated boxes of water and LC. After a steep simulation of about 1,000,000 steps I try to do an md simulation but I get the error "Water molecule starting

RE: [gmx-users] Re: v-rescale - harmonic oscillator

Hi, That is a fundamental problem of most global thermostats, just like Nose-Hoover. Nose-Hoover chains solve this. The only thermostats that guarantee proper ensembles for any system are local ones such as Langevin dynamics. Berk > From: servaas.michielss...@student.kuleuven.be > To: gmx-users

[gmx-users] Re: v-rescale - harmonic oscillator

Hi, Thanks for your confirmation of this problem. One thing is not clear to me from your answer. Has v-rescale fundamental problems with a Harmonic oscillator or is it a problem with the GROMACS implementation? Kind regards, Servaas > Message: 3 > Date: Fri, 8 May 2009 10:12:45 +0200 > From:

[gmx-users] x2top and OPLS-AA vs. fudged 1-4 interactions

Dear colleagues, I'm looking for clarifications on what exactly I need to do in order to get a correct scaling of 1-4 interactions for OPLS-AA in a topology made by x2top. Specifically, will the command x2top -f in.gro -o out.top result in a topology that, when fed into grompp, will give a .tpr

[gmx-users] (no subject)

Dear all, I am trying to simulate a water-liquid crystal system. My initial is box is creating by merging two well equilibrated boxes of water and LC. After a steep simulation of about 1,000,000 steps I try to do an md simulation but I get the error "Water molecule starting at atom 9103 can no

RE: [gmx-users] Re: v-rescale - harmonic oscillator

Hi, I have come to the conclusion that the v-rescale thermostat is only correct in the limit of large numbers of degrees of freedom, which is equivalent to a small scaling limit. The conservation of the conserved energy quantity improves as the system gets bigger. But I noticed that in 4.0 the

[gmx-users] updated OPLS/AA

Can someone confirm that GMX 4.x is already released with updated OPLS/AA files as once mentioned in http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,7/Itemid,26/ ? Many thanks in advance. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Bio

Re: [gmx-users] How to set up the cut-off radius

Hi, Yanmei On Fri, May 8, 2009 at 2:20 AM, Yanmei Song wrote: > NOTE 2 [file aminoacids.dat, line 1]: > The optimal PME mesh load for parallel simulations is below 0.5 > and for highly parallel simulations between 0.25 and 0.33, > for higher performance, increase the cut-off and the PME gr