Re: [gmx-users] LINCS error

I get an error like this= Step 43230, time 86.46 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.033583, max 1.621884 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.0

Re: [gmx-users] LINCS error

aiswarya pawar wrote: I get an error like this= Step 43230, time 86.46 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.033583, max 1.621884 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length

[gmx-users] LINCS error

Hi users, I did energy minimization of a protein complex using the following minimization mdp file. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to

Re: [gmx-users] LINCS error

On 19/12/2011 1:05 AM, aiswarya pawar wrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation for general advice. ; Lines starting with ';' ARE COMMENTS ;

Re: [gmx-users] LINCS error- 4.5.4 installation?

On 4/30/2011 9:06 AM, Juliette N. wrote: Dear experts, I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few steps I get LINCS error: step 400, will finish Sat Apr 30 05:20:45 2011 Step 750, time 1.5 (ps) LINCS WARNING relative constraint deviation after LINCS: rms

Re: [gmx-users] LINCS error

Yongchul Chung wrote: Hi again gmx-users, I ran into LINCS error again when I tried to incorporate pressure scaling parameters. It seems like the initial pressure and temperature is erroneously large as shown in the md.log file below. can anyone tell me how to fix this? Did you run

Re: [gmx-users] LINCS error

Yongchul Chung wrote: yes I carried out energy minimization and used following parameters. OK, so what values of potential energy and maximum force did EM achieve? -Justin title = FWS cpp = /usr/bin/cpp ; the c pre-processor define =

Re: [gmx-users] LINCS error

After EM, I got: Potential Energy = 1.7242092e+05 Maximum force = 2.1079963e+03 on atom 675 Norm of force = 5.9417034e+01 I think my system size is too big compared to the box size so I am going to run the simulation with smaller number of molecules to see whether this helps or not.

Re: [gmx-users] LINCS error

Yongchul Chung wrote: After EM, I got: Potential Energy = 1.7242092e+05 Maximum force = 2.1079963e+03 on atom 675 Norm of force = 5.9417034e+01 I think my system size is too big compared to the box size so I am going to run the simulation with smaller number of molecules to see

[gmx-users] LINCS error

Hi all, I am trying to simulate 100 molecules of n-alkane molecules but keep receiving LINC errors. When I completed steepest descent I received following msg: Steepest Descents converged to Fmax 500 in 819 steps Potential Energy = 1.7174361e+05 Maximum force = 4.4903098e+02 on atom 172

Re: [gmx-users] LINCS error

delta_t = 0.01 You are using a 10 fs timestep!!! That is way too long. Standard is 2 (with bond constraints). Yongchul Chung wrote: Hi all, I am trying to simulate 100 molecules of n-alkane molecules but keep receiving LINC errors. When I completed steepest descent I

Re: [gmx-users] LINCS error

Hi guys, As Justin pointed out, it was the problem with md simulation blowing up. I also had coloumbtype=PME and had to switch to cut-off to make my simulation run faster. Thanks for all the help. On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub joc...@xray.bmc.uu.se wrote: delta_t

Re: [gmx-users] LINCS error

Yongchul Chung wrote: Hi guys, As Justin pointed out, it was the problem with md simulation blowing up. I also had coloumbtype=PME and had to switch to cut-off to make my simulation run faster. And it will be substantially less accurate than using PME. I would say Jochen's advice is

[gmx-users] LINCS error

 Hi, I am trying to simulate a peptide whose structure is yet to be validated experimentally. It has 3 protonated lysine residues. I have used oplsaa force filed with spc water model and had added 3 CL ions into the box. Everything works fine till energy minimisation but after that

Re: [gmx-users] LINCS error

sarbani chattopadhyay wrote: Hi, I am trying to simulate a peptide whose structure is yet to be validated experimentally. It has 3 protonated lysine residues. I have used oplsaa force filed with spc water model and had added 3 CL ions into the box. Everything works fine till energy

[gmx-users] Lincs error and explosion of the system

Dear users, I have a problem on runningMD of 146 LC molecules system. I do not do the energy minimisation. I use NVT ensemble to equilibrate my system.My topology was created using PRODRG beta server. After the creation of my systems box (on top of each other) 1. editconf -f lc -bt d -box 1.3

Re: [gmx-users] Lincs error and explosion of the system

Why don't you do energy minimization? It's pretty clear that you've generated some atomic overlap in your procedure, from what you've described. For general reference on such problems, check the hundreds of related posts (LINCS warnings) in the list archive or the following link to the wiki

[gmx-users] LINCS error

hello users, i am using gromacs 3.3 version on unix platform i got these error while running MD simulation of 89 aa in spc216 water for 10ns at step 4088373 time 8176.55 .i had used force field 4a1(official distribution) hear I'm sending .mdp file also error which i got is

Re: [gmx-users] LINCS error

This is an issue that has been discussed a lot on the list. The typical reasons for LINCS errors can be found here: http://wiki.gromacs.org/index.php/Errors#LINCS_warnings Quoting vijay kumar hinge vijay [EMAIL PROTECTED]: hello users, i am using gromacs 3.3 version on unix platform i got

Re: [gmx-users] LINCS error during mdrun

Mark Abraham a écrit : Dear GROMACS users, I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING I looked up the mailing list and

Re: [gmx-users] LINCS error during mdrun

Dear GROMACS users, I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING I looked up the mailing list and found discussion

Re: [gmx-users] LINCS error during mdrun

Hi Shangwa Han, First of all, there is no general conclusion regarding such error. Second, the general conclusion is: your system contains severe errors, which have not been resolved during energy minimization, if you performed any, but you didn't mention it. If you would have browsed the

[gmx-users] LINCS error during mdrun

Dear GROMACS users, I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING relative constraint deviation after LINCS: max

[gmx-users] lincs error

Hi! this is my problem: after a few step (from 1 to 20) mdrun stops because of lincs ...LINCS WARNING - Relative constraint deviation after lincs: max 103.684275 (between atoms 7941 and 7942) rms 1.227871 bonds that rotated more than 180 degrees... 7941 e 7942 should be two water atoms.

[gmx-users] LINCS Error in Gromacs-3.3.1 in pr simulation

Dear all, I have been trying to simulate various mutant models (single mutant) of a enzyme. I am successfully finished simulation of 3 variants including wild type (So for finished up to position restraints of all variants). In one mutation involving Ala in requsite