Re: [gmx-users] gromacs 4.0.3 tests validations

Hi, I think the tests for pdb2gmx are outdated. Most fail due to warning(s) while running grompp, which were allowed with older versions. I'm not sure who maintains this tests - maybe a new version is due. Ran. Tru Huynh wrote: > Hi, > > I am compiling gromacs on CentOS-3 x86_64 both serial and LA

[gmx-users] template

Hi, Dear Gromacs users, I try to compile gromacs template by typing "make template" as said in gromacs FAQ, but I have a lot of errors. > make template > cc template.c -o template > template.c:40:22: error: statutil.h: No such file or directory > template.c:41:22: error: typedefs.h: No such

[gmx-users] Problem with continuation of files using checkpoint files

Dear All, I am doing protein simulations using Gromacs4.0.2. For continuation or extension of runs, i am using tpbconv command. In the manual its given that for exact binary identical run, one needs to use checkpoint file with mdrun. So, for the tpbconv generated file when I am using checkpoint. I

[gmx-users] PR dynamics

Hi we are simulating a protein of 260 a.a length which is a trimer...How does the MDRUN time during the PR affects the Full Dynamics results??? Lucky ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-use

[gmx-users] position restraint dynamics

Hi..dear gromacs users...How do we decide the ideal time to run PR??we are simulating a protein of 260 amino acids which is a tirmer...we have done the PR for 10 ps first time and 100ps for the second ...i had observed a stable graph in the latter compared with the other...and on what factors does

RE: [gmx-users] Problem with continuation of files using checkpoint files

Hi, This means that your checkpoint file was generated with a single processor simulation, while you are now running a two processor simulation. This is no problem at all. For the 4.0.4 release I changed: "Continuation still works," to "Continuation is exact," Note that you don't need -f and -e

Re: [gmx-users] position restraint dynamics

bhargavi ch wrote: Hi..dear gromacs users...How do we decide the ideal time to run PR??we are simulating a protein of 260 amino acids which is a tirmer...we have done the PR for 10 ps first time and 100ps for the second ...i had observed a stable graph in the latter compared with the other

[gmx-users] (no subject)

Dear gromacs-users, I am heating a peptidein methanol from 0K - 300K. The simulated annealing protocol is given in the md.mdp file shown below: title = cpeptide MD cpp = /lib/cpp constraints = all-bonds in

Re: [gmx-users] (no subject)

I don't have so much experience, but I found something strange in our mdp file. >; Berendsen temperature coupling is on in two groups > Tcoupl = no > tau_t = 0 0 In my opinion, I think that if you have Tcoupl = no you can't expect the temperature of your sys

Re: Re: [gmx-users] SIMULATED ANNEALING

Dear Nuno Azoia, I followed one of the replies given at gmx-users list which I quote here...I donot know whether this is right ? In that case the temperature has truly changed from 0 to 60 how is it possible if Tcoupl = no...?I am in doubt. Kindly comment. sharada Re: [gmx-users] how to write a

Re: [gmx-users] gromacs 4.0.3 tests validations

On Thu, Feb 12, 2009 at 09:19:29AM +0100, Ran Friedman wrote: > Hi, > I think the tests for pdb2gmx are outdated. Most fail due to warning(s) > while running grompp, which were allowed with older versions. > I'm not sure who maintains this tests - maybe a new version is due. thanks for the reply.

Re: [gmx-users] gromacs 4.0.3 tests validations

Tru Huynh wrote: On Thu, Feb 12, 2009 at 09:19:29AM +0100, Ran Friedman wrote: Hi, I think the tests for pdb2gmx are outdated. Most fail due to warning(s) while running grompp, which were allowed with older versions. I'm not sure who maintains this tests - maybe a new version is due. thanks f

Re: [gmx-users] template

Alexander Malafeev wrote: Hi, Dear Gromacs users, I try to compile gromacs template by typing "make template" as said in gromacs FAQ, but I have a lot of errors. You still need to have used "configure" to generate a proper Makefile. All of these errors are happening because you haven't told th

Re: [gmx-users] SIMULATED ANNEALING

sharada wrote: Dear Nuno Azoia, I followed one of the replies given at gmx-users list which I quote here...I donot know whether this is right ? In that case the temperature has truly changed from 0 to 60 how is it possible if Tcoupl = no...?I am in doubt. You're actually running in an NVE

Re: [gmx-users] gromacs 4.0.3 tests validations

Justin A. Lemkul wrote: Tru Huynh wrote: On Thu, Feb 12, 2009 at 09:19:29AM +0100, Ran Friedman wrote: Hi, I think the tests for pdb2gmx are outdated. Most fail due to warning(s) while running grompp, which were allowed with older versions. I'm not sure who maintains this tests - maybe a new

[gmx-users] mass of a index group

Hi users! Is there a gmx tool, which calculates the mass of one or more index groups? The manual says something about a tool named "g_com", but it seems, as if it does not belong to gmx4.0.3 anymore. Greetings, Christian. -- M. Sc. Christian Seifert Department of Biophysics University of Bochu

Re: [gmx-users] mass of a index group

Christian Seifert wrote: Hi users! Is there a gmx tool, which calculates the mass of one or more index groups? The manual says something about a tool named "g_com", but it seems, as if it does not belong to gmx4.0.3 anymore. try g_traj Greetings, Christian. -- David van der Spoel, Ph.D.,

Re: [gmx-users] mass of a index group

Hi David, after reading the man page of g_traj and some tests on its output, I can not discover a way of getting the total mass of an index group (e.g. protein). Cheers, Christian. On Thu, 2009-02-12 at 14:35 +0100, David van der Spoel wrote: > Christian Seifert wrote: > > Hi users! > > > > Is

Re: [gmx-users] template

2009/2/12 Mark Abraham > Alexander Malafeev wrote: > >> Hi, Dear Gromacs users, I try to compile gromacs template by typing "make >> template" as said in gromacs FAQ, but I have a lot of errors. >> > > You still need to have used "configure" to generate a proper Makefile. All > of these errors ar

Re: [gmx-users] mass of a index group

Christian Seifert wrote: Hi David, after reading the man page of g_traj and some tests on its output, I can not discover a way of getting the total mass of an index group (e.g. protein). The total mass of the protein is printed by pdb2gmx. Otherwise you can process your topology using a P

[gmx-users] Physical problems of comm removal

Hi users! I simulate a stretched protein in TIP4P water in a cubic box (6.83x9.60x13.58=890) with pbc. During a 50 ns simulation, my protein must not rotate (otherwise, it will interact with itself). I found three possibilities to avoid a self interaction: (1) a bigger box, (2) restraints or (3) c

RE: [gmx-users] Physical problems of comm removal

Hi, The cleanest solution is using a rhombic dodecahedron: volume 13.58^3/sqrt(2) = 1771 nm^3 (I don't know why people still consider truncated octahedrons). You can try using comm-mode=angular with as comm group only the protein. This should not produce significant artifacts when your protein i

Re: [gmx-users] mass of a index group

On Thu, 2009-02-12 at 09:28 -0500, Justin A. Lemkul wrote: > > Christian Seifert wrote: > > Hi David, > > > > after reading the man page of g_traj and some tests on its output, I can > > not discover a way of getting the total mass of an index group (e.g. > > protein). > > > > The total mass of

RE: [gmx-users] Physical problems of comm removal

Hi Berk, the rhombic dodecahedron with 1771 nm^3 is still twice as big as my stretched box. This System scales quite well till 256 CPUs and I normally use this amount of CPUs (I have to hurry up with my PhD thesis), so particle decomposition is not an alternative. Are there other alternatives?

RE: [gmx-users] Physical problems of comm removal

Hi, Another crude solution is to divide your protein into two groups along the long axis and use the pull code to keep the two components perpendicular to the axis of the vector between the COMs at zero. PS: if you have PME your system will run faster when you make x the long axis. Berk > Dat

RE: [gmx-users] Physical problems of comm removal

Thanks for your ideas! I will discuss the possible solutions with my supervisor. To your PS: This is a good hint, I changed many optimization flags to get a good scaling but never changed the axis. I created the box with editconf -princ. It automatically made z the longest axis and x the shortest

Re: [gmx-users] gromacs 4.0.3 tests validations

Justin A. Lemkul wrote: Tru Huynh wrote: On Thu, Feb 12, 2009 at 09:19:29AM +0100, Ran Friedman wrote: Hi, I think the tests for pdb2gmx are outdated. Most fail due to warning(s) while running grompp, which were allowed with older versions. I'm not sure who maintains this tests - maybe a new

RE: [gmx-users] Physical problems of comm removal

> Date: Thu, 12 Feb 2009 16:49:33 +0100 > From: cseif...@bph.ruhr-uni-bochum.de > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Physical problems of comm removal > > Thanks for your ideas! > > I will discuss the possible solutions with my supervisor. > > To your PS: > This is a good hi

[gmx-users] position restraint dynamics

Hi we are simulating a protein of 260 a.a length which is a trimer...How does the mdrun time during the position restraint dynamics affects the Full Dynamics results??? Regards Bhargavi ___ gmx-users mailing listgmx-users@gromacs.org http://www.

Re: [gmx-users] P-N vector orientation

Hello, I just remember that you might be interested by g_tilt developed by Patrick Fuchs.: http://www.dsimb.inserm.fr/~fuchs/download/ Its purpose is to calculate the orientation of an helix in a bilayer, however it might tweaked to calcu

[gmx-users] position restraint dynamics

If you want to know how much time is required for this step (assuming that this step is even required) then that is system dependent and something that you would ideally test for yourself. For example, after N ps of position restrained dynamics, how does that affect the RMSD of the protein

RE: [gmx-users] P-N vector orientation

Hi, g_bundle does something similar, so does g_sgangle (but only for one vector I think). Berk > Date: Thu, 12 Feb 2009 10:50:02 -0700 > From: nsa...@ucalgary.ca > To: aninditaga...@yahoo.co.in; gmx-users@gromacs.org > Subject: Re: [gmx-users] P-N vector orientation > CC: > > Hello, > > I ju

Re: [gmx-users] Physical problems of comm removal

Berk Hess wrote: > Date: Thu, 12 Feb 2009 16:49:33 +0100 > From: cseif...@bph.ruhr-uni-bochum.de > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Physical problems of comm removal > > Thanks for your ideas! > > I will discuss the possible solutions with my supervisor. > > To y

Re: [gmx-users] Physical problems of comm removal

On Feb 12, 2009, at 8:03 PM, Justin A. Lemkul wrote: Berk Hess wrote: > Date: Thu, 12 Feb 2009 16:49:33 +0100 > From: cseif...@bph.ruhr-uni-bochum.de > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Physical problems of comm removal > > Thanks for your ideas! > > I will discuss the pos

[gmx-users] pull code, lambda, and soft core availability

Hello, I see from looking at the source code that the free-energy lambda dependence is now available to the pull code based on pull_kB1. However, this leads to serious problems converging near lambda=1 when pull_k1=large and pull_kB1=0 and in the absence of a restraint (with k=0) the pull

Re: [gmx-users] pull code, lambda, and soft core availability

This seems to be a good reference for soft-core interactions. BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys Lett (1994) vol. 222 pp. 529-539 On Thu, Feb 12, 2009 at 1:33 PM, wrote: Does anybody know of a

[gmx-users] pull code, lambda, and soft core availability

Thank you Matt, that is indeed the perfect paper. I'll post back here once I figure out exactly where the (1-lambda)^2 term would fit into the pull code US equation. Chris. This seems to be a good reference for soft-core interactions. BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INST

[gmx-users] checkpoint

Hi! I recently installed GROMACS 4.0 and in the md.log file (pasted below) I found the "writing check point" statement. This was not there in the previous versions of GROMACS. Is this to be expected or is this an indication that some thing is going wrong? Thanks JJ Writing checkpoint, step

Re: [gmx-users] checkpoint

Quoting jayant james : > Hi! > I recently installed GROMACS 4.0 and in the md.log file (pasted below) I > found the "writing check point" statement. This was not there in > the previous versions of GROMACS. Is this to be expected or is this an > indication that some thing is going wrong?

RE: [gmx-users] 4.0.3 goes off into la la land .... infinite loop

I have submitted a bugzilla on this issue ... http://bugzilla.gromacs.org/show_bug.cgi?id=296 Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation <>__

Re: [gmx-users] template

Alexander Malafeev wrote: 2009/2/12 Mark Abraham > Alexander Malafeev wrote: Hi, Dear Gromacs users, I try to compile gromacs template by typing "make template" as said in gromacs FAQ, but I have a lot of errors. You still nee

[gmx-users] Problem with decane box

I am trying to set up a system with a helix in a decane box. I am using dec50.gro and decane.itp files to build the box. I've used GROMOS96 53a6 forcefield and when I run grompp the following error comes out. ERROR 0 [file "vegfr2.top", line 37]: atom C10 (Res C10-107) has mass 0 -

[gmx-users] pull code, lambda, and soft core availability

Upon further investigation, it appears that a soft core may help in this case. This is in spite of the fact that the problem is not a singularity, but that the dgdl term (dgdl=0.5*(Fc_B-Fc_A)*(r-r0)^2) gives very large values for Fc_A large enough to be significantly restraining and Fc_B =

Re: [gmx-users] Problem with decane box

Ragnarok sdf wrote: I am trying to set up a system with a helix in a decane box. I am using dec50.gro and decane.itp files to build the box. I've used GROMOS96 53a6 forcefield and when I run grompp the following error comes out. Hopefully you have modified the decane.itp that you found in th

Re: [gmx-users] g_wham Error bars

Hello, As far as I know, it is not possible to directly calculate and error bar with g_wham . At that point, you've got several options: 1) You can run several times your umbrella sampling simulations, calculate several PMFs, then calculate an average and a standard deviation 2) i

[gmx-users] g_wham Error bars

In addition to the suggestions made by Nicolas, you might try the wham program created by Alan Grossfield: http://membrane.urmc.rochester.edu/Software/WHAM/WHAM.html which is capable of doing a 'bootstrap' analysis of the error. If you have the available computational resources, then I beli

Re: Re: [gmx-users] SIMULATED ANNEALING

Thankyou for the reply Mark. In fact I started another simulated annealing job for my peptide with Tcoupl = Berendsen using the same annealing protocol. I didnot get any warnings. However the temperature increases from 0 to 53K and fluctuates around that through out till the end of the simulati