[gmx-users] testing gromacs runs
Dear all, I have just installed gromacs 4.6.5 in Cygwin build on Windows 7 platform. I want to test the installation but it keeps giving the error ./gmxtest.pl all ERROR: Can not find executable gmx pdb2gmx in your path. Please source GMXRC and try again. My Gromacs is installed in the C: drive outside the root. I have also put the regression folder downloaded from http://gerrit.gromacs.org/download/regressiontests-4.6.5.tar.gz I sourced gromacs from inside the folder where the file gmxtest.pl is. However when i want execute pdb2gmx, the file executes Could you guide please? thank you Ayesha -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv_d errors
Dear All, I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping there was adifference) as I am using terra grid with a 5.0.1 install. Now, I noticed 2 things, trjconv_d no matter what I do can not read or convert the .trr file, even with simple -f in.trr -o out.trr or .xtc files. I was simply interested mostly as my secound problem is, if I include anything other than the standard energy groups of protein non_protein (say x y z), the performance goes from 20 ns a day for my system, to 10 ns a day. Thus I was going to rerun everything after the grid usage with -rerun and a changed energy group list just to make my life easier. I checked all of this with 4.5.6, 4.6.7 versions and the trjconv_d -f in.trr -o out.trr or out.xtc works fine. It will even process a standard 5.0.1 in.trr file, however if I then try any type of rerun (as expected) I get a version error. Is this a) a bug and b) a if so or not, does someone have a work around? I have also tried gmx_d trjconv, and I searched the mail archives, and the only thing anyone mentioned was a 64 bit, vs a 32 bit Linux install delema, stating if the files were larger than a few gigs, there was a memory error. I origionally thought this the error, however decided to run test first with small 100MB-2 G runs to test it, and this was not the problem. Sincerely, Stephan L. Watkins, PhD -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] periodic boundary conditions pbc=xyz
Hi Ming Use *-pbc mol* while using trjconv. Anyway it is not another box. Best Regards -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB, INDIA -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simultaneous runs
On 4/5/15 1:10 AM, mah maz wrote: Dear all, I performed 2 runs one after the other. Then, I performed those 2 runs simultaneously(no special commands were applied, I just used different terminals with mdrun -v command) but in different directories. Results (like msd and energies) were expected to be nearly the same. but they are completely different. Does it mean that we cant perform several runs simultaneously? Independent runs have no effect on each other. All you're seeing is the random nature of MD. http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] periodic boundary conditions pbc=xyz
Dear all, I did a simulation using periodic boundary conditions pbc=xyz. It turns out that the box is defined too small, and some atoms go to another box. Does this affect the simulation result? If not, how to display the real model (without separation) in VMD? Thanks in advance, Ming -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] periodic boundary conditions pbc=xyz
Hi Ming, You have another box in your (infinite) periodic system? Cheers, Tsjerk On Sun, Apr 5, 2015 at 10:32 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I did a simulation using periodic boundary conditions pbc=xyz. It turns out that the box is defined too small, and some atoms go to another box. Does this affect the simulation result? If not, how to display the real model (without separation) in VMD? Thanks in advance, Ming -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] periodic boundary conditions pbc=xyz
Hi Tsjerk, I defined only one box. I mean several atoms in one chain run out of the boundary, and I can see them in the box but not in the chain. So I think maybe they run to the nearby box because of the periodic boundary conditions. Thanks, Ming -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Sunday, 5 April 2015 7:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] periodic boundary conditions pbc=xyz Hi Ming, You have another box in your (infinite) periodic system? Cheers, Tsjerk On Sun, Apr 5, 2015 at 10:32 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I did a simulation using periodic boundary conditions pbc=xyz. It turns out that the box is defined too small, and some atoms go to another box. Does this affect the simulation result? If not, how to display the real model (without separation) in VMD? Thanks in advance, Ming -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] simulating liquid SO2 (Sulphur dioxide)
Dear gromacs users, I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create an equilibrated structure of SO2 molecules using the gmx insert-molecules function. As I try to minimize the energy of the system, I always get this- Energy minimization has stopped, but the forces have not converged to the requested precision Fmax 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. I tried to analyze my .gro file that the gmx insert-molecules function is returning me and found that some of my SO2 have a bond in between them. Is this what causes the energy minimization to crash? Is there any way I can prepare an equilibrated system of liquid SO2 ? My SO2.itp file is like this (I made this an .itp because I wish to study this system along with some other molecules)- [ moleculetype ] ; Name nrexcl SO23 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_202 1 SR S 1 0.6512 32.07 ;qtot 0.6512 2 opls_326 1 SR O1 2-0.3256 15.99940 ;qtot 0.3256 3 opls_326 1 SR O2 3-0.3256 15.99940 ; qtot 0 ; opls_202 S 16 32.07 0.6512 A3.61500e-01 1.2125232 ; opls_326 O 8 15.99940-0.3256 A3.00500e-01 0.47756176 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 0.1434 635968.0 1 3 1 0.1434635968.0 [ distance_restraints ] ; aiaj type index type' low up1 up2 fac 1 2 1 0 1 1.149 1.490 1.490 1.0 1 3 1 0 1 1.149 1.490 1.490 1.0 [ angles ] ; aiajak functc0c1 c2c3 2 1 3 1119.51359.8 I have also uploaded the .gro file that the gmx insert-molecules function is returning me after this text. SO2_box300.gro https://docs.google.com/file/d/0B8p1k0KkNddyUEN3dzZRZE5keXM/edit?usp=drive_web Thanks in advance. -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulating liquid SO2 (Sulphur dioxide)
Em 05/04/2015 14:44, Jashimuddin Ashraf jashimuddin.ashra...@gmail.com escreveu: Dear gromacs users, I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create an equilibrated structure of SO2 molecules using the gmx insert-molecules function. As I try to minimize the energy of the system, I always get this- Energy minimization has stopped, but the forces have not converged to the requested precision Fmax 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. That isn't necessarily a problem here, unless the maximum force is too high. You have requested a low threshold (emtol =10) and the machine precision can't reach it on simple precision. I tried to analyze my .gro file that the gmx insert-molecules function is returning me and found that some of my SO2 have a bond in between them. Is this what causes the energy minimization to crash? Also, the .gro file just outputs atoms coordinates. There is no 'bonds' on it. Usualy, that is a visualization problem. Is there any way I can prepare an equilibrated system of liquid SO2 ? Yes. Read the paper 'Force field benchmark for organic liquids' and you might get an idea how to do it. My SO2.itp file is like this (I made this an .itp because I wish to study this system along with some other molecules)- [ moleculetype ] ; Name nrexcl SO23 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_202 1 SR S 1 0.6512 32.07 ;qtot 0.6512 2 opls_326 1 SR O1 2-0.3256 15.99940 ;qtot 0.3256 3 opls_326 1 SR O2 3-0.3256 15.99940 ; qtot 0 ; opls_202 S 16 32.07 0.6512 A3.61500e-01 1.2125232 ; opls_326 O 8 15.99940-0.3256 A3.00500e-01 0.47756176 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 0.1434 635968.0 1 3 1 0.1434635968.0 [ distance_restraints ] ; aiaj type index type' low up1 up2 fac 1 2 1 0 1 1.149 1.490 1.490 1.0 1 3 1 0 1 1.149 1.490 1.490 1.0 [ angles ] ; aiajak functc0c1 c2c3 2 1 3 1119.51359.8 I have also uploaded the .gro file that the gmx insert-molecules function is returning me after this text. SO2_box300.gro https://docs.google.com/file/d/0B8p1k0KkNddyUEN3dzZRZE5keXM/edit?usp=drive_web Thanks in advance. -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
