On 8/1/17 6:07 PM, Ali Ahmed wrote:
Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Here is what I get before crashing. Too many warning then crush.
This is not diagnostic of anything useful. You've been asked several times to
provide the output of grompp, not mdrun. The grompp output can be suggestive of
issues you may not have considered.
-Justin
Step 37, time 0.037 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002768, max 0.195102 (between atoms 34930 and 34931)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
193 194 51.7 0.1100 0.1100 0.1100
54409 54410 32.3 0.1100 0.1100 0.1100
On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren <dallas.war...@monash.edu>
wrote:
Copy the output from both of those commands, most importantly (as Mark
has asked) that from the first one gmx grompp
You need to show people exactly what you are seeing, not what you say
you are seeing. The latter you are filtering it, and most likely not
providing all the important information. The former allows those
trying to help to see all the information that they need to see.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
On 2 August 2017 at 04:05, Ali Ahmed <aa5635...@gmail.com> wrote:
Hi,
Thank you for your help.
well I used this command
gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em
and I got all the warnings. Here is my em.mdp
------------------------------------------------------------
-------------------------
integrator = steep
emtol = 10.0
emstep = 0.001
nsteps = 50000
energygrps = system
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1
cutoff-scheme = group
ns_type = grid
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
No, only mdrun issues LINCS warnings. grompp issues different warnings,
and
I would like you to check whether you had any from grompp that you may
not
have considered. :-)
Mark
On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed <aa5635...@gmail.com> wrote:
Dear Mark
Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you
On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <
mark.j.abra...@gmail.com>
wrote:
Hi,
Did you get any warnings from grompp?
Mark
On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed <aa5635...@gmail.com>
wrote:
Hello GROMACS users,
I'm doing MD for nitrogen, and for better electrostatic
interactions
I
need
to use massless and charged virtual site. I did that but when I
try
to
do
energy minimization gives me LINCS warning and crush. I don't know
where
is
the error I tried a lot but could not find a solution.
Anyone has an idea where is my error
Here is the topology file (hand written)
------------------
[ defaults ]
1 3 yes 0.5 0.5
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;
[ atomtypes ]
; name bond_type mass charge ptype sigma
epsilon
OP OP 0.000 0.000 A 0.330
0.3062
;
nitrogen
M M 0.000 0.000 V 0.000
0.000
;
virtual site
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;
[ moleculetype ]
; name nrexcl
N2 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OP 1 N2 N1 1 -0.482
14.0067
2 M 1 N2 M1 1 0.964 0.000
3 OP 1 N2 N2 1 -0.482
14.0067
[ constraints ]
; the N-N is fixed
1 3 1 0.11
[ virtual_sites2 ]
; site ai aj funct a
2 1 3 1 0.5000 ; right in the mid
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
[ system ]
N2 in vacuo
[ molecules ]
N2 1500
------------------------------------------------------------
--------------------------------------
Here is the structure (N2.pdb)
-----------
TITLE N2 with dummy masses
REMARK THIS IS A SIMULATION BOX
MODEL 1
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.2
CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1
1
ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00
0.00 N
ATOM 2 M1 N2 1 0.55000 0.000 0.000 1.00
0.00 Xx
ATOM 3 N2 N2 1 1.100 0.000 0.000 1.00
0.00 N
CONECT 1 3
CONECT 3 1
MASTER 0 0 0 0 0 0 0 0 3 0 3
0
END0
------------------------------------------------------------
---------------------------------
Thank you
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--
==================================================
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
==================================================
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